(used for variant description)
(last modified March 5, 2017)
This file was created to facilitate the description of sequence variants on transcript NM_152989.3 in the SOX5 gene based on a coding DNA reference sequence following the HGVS recommendations.
The sequence was taken from NG_029612.1, covering SOX5 transcript NM_152989.3.
(upstream sequence)
. g.5011
agagtgaaaaaggc c.-361
. . . . . . g.5071
gagccaccaaaacccatctccagtctcctcccgggggcccccagcccgcctctgtgccac c.-301
. . . . . | 02 . g.159897
tttgcatcccacgccggaggaggcattaacgagaccgggtaag | gctttttaaacggtcca c.-241
. . . . . . g.159957
aggtgtagagccatacttcaggaggatcctcagaagttttggacaagcctccccaaatgt c.-181
. | 03 . . . . . g.198862
ggcag | gtgctgtgctggccattggtgacccaaagatgatgaaaaatatgttcctgcccac c.-121
. . . | 04 . . . g.290172
aaggagttagcgacctactggg | ctttcctcttgctgatgacatgattcctgtttgaatct c.-61
. . . . . . | 05 g.671423
gttgacaagattctgaaagctgaacagagaattctggcactgcactgggtaggaaaaag | g c.-1
. . . . . . g.671483
ATGTCTTCCAAGCGACCAGCCTCTCCGTATGGGGAAGCAGATGGAGAGGTAGCCATGGTG c.60
M S S K R P A S P Y G E A D G E V A M V p.20
. . . . . . g.671543
ACAAGCAGACAGAAAGTGGAAGAAGAGGAGAGTGACGGGCTCCCAGCCTTTCACCTTCCC c.120
T S R Q K V E E E E S D G L P A F H L P p.40
. . . . . . g.671603
TTGCATGTGAGTTTTCCCAACAAGCCTCACTCTGAGGAATTTCAGCCAGTTTCTCTGCTG c.180
L H V S F P N K P H S E E F Q P V S L L p.60
. . . . . | 06 . g.721262
ACGCAAGAGACTTGTGGCCATAGGACTCCCACTTCTCAGCACAATACAATG | GAAGTTGAT c.240
T Q E T C G H R T P T S Q H N T M | E V D p.80
. . . . . . g.721322
GGCAATAAAGTTATGTCTTCATTTGCCCCACACAACTCATCTACCTCACCTCAGAAGGCA c.300
G N K V M S S F A P H N S S T S P Q K A p.100
. . . . . . g.721382
GAAGAAGGTGGGCGACAGAGTGGCGAGTCCTTGTCTAGTACAGCCCTGGGAACTCCTGAA c.360
E E G G R Q S G E S L S S T A L G T P E p.120
. . . . . . g.721442
CGGCGCAAGGGCAGTTTAGCTGATGTTGTTGACACCTTGAAGCAGAGGAAAATGGAAGAG c.420
R R K G S L A D V V D T L K Q R K M E E p.140
. . | 07 . . . . g.811760
CTCATCAAAAACGAGCCGGAAG | AAACCCCCAGTATTGAAAAACTACTCTCAAAGGACTGG c.480
L I K N E P E E | T P S I E K L L S K D W p.160
. . . . | 08 . g.826418
AAAGACAAGCTTCTTGCAATGGGATCGGGGAACTTTGGCGAAATAAAAG | GGACTCCCGAG c.540
K D K L L A M G S G N F G E I K G | T P E p.180
. . . . . . g.826478
AGCTTAGCTGAGAAAGAAAGGCAACTCATGGGTATGATCAACCAGCTGACCAGCCTCCGA c.600
S L A E K E R Q L M G M I N Q L T S L R p.200
. . . . . . g.826538
GAGCAGCTGTTGGCTGCCCACGATGAGCAGAAGAAACTAGCTGCCTCTCAGATTGAGAAA c.660
E Q L L A A H D E Q K K L A A S Q I E K p.220
. . . . | 09 . . g.832712
CAGCGTCAGCAAATGGAGCTGGCCAAGCAGCAACAAGAACAA | ATTGCAAGACAGCAGCAG c.720
Q R Q Q M E L A K Q Q Q E Q | I A R Q Q Q p.240
. . . . . | 10 . g.901891
CAGCTTCTACAGCAACAACACAAAATCAATTTGCTCCAGCAACAGATCCAG | GTTCAAGGT c.780
Q L L Q Q Q H K I N L L Q Q Q I Q | V Q G p.260
. . . . . . g.901951
CAGCTGCCGCCATTAATGATTCCCGTATTCCCTCCTGATCAACGGACACTGGCTGCAGCT c.840
Q L P P L M I P V F P P D Q R T L A A A p.280
. . . . . | 11 . g.926557
GCCCAGCAAGGATTCCTCCTCCCTCCAGGCTTCAGCTATAAGGCTGGATGTA | GTGACCCT c.900
A Q Q G F L L P P G F S Y K A G C S | D P p.300
. . . . . . g.926617
TACCCTGTTCAGCTGATCCCAACTACCATGGCAGCTGCTGCCGCAGCAACACCAGGCTTA c.960
Y P V Q L I P T T M A A A A A A T P G L p.320
. | 12 . . . . g.962955
GGCCCACTCCAACTGCAG | CAGTTATATGCTGCCCAGCTAGCTGCAATGCAGGTATCTCCA c.1020
G P L Q L Q | Q L Y A A Q L A A M Q V S P p.340
. . . . . . g.963015
GGAGGGAAGCTGCCAGGCATACCCCAAGGCAACCTTGGTGCTGCTGTATCTCCTACCAGC c.1080
G G K L P G I P Q G N L G A A V S P T S p.360
. . . . | 13 . . g.991623
ATTCACACAGACAAGAGCACAAACAGCCCACCACCCAAAAGCAAG | GATGAAGTGGCACAG c.1140
I H T D K S T N S P P P K S K | D E V A Q p.380
. . . . . . g.991683
CCACTGAACCTATCAGCTAAACCCAAGACCTCTGATGGCAAATCACCCACATCACCCACC c.1200
P L N L S A K P K T S D G K S P T S P T p.400
. . . . . . g.991743
TCTCCCCATATGCCAGCTCTGAGAATAAACAGTGGGGCAGGCCCCCTCAAAGCCTCTGTC c.1260
S P H M P A L R I N S G A G P L K A S V p.420
. . . . | 14 . . g.1004060
CCAGCAGCGTTAGCTAGTCCTTCAGCCAGAGTTAGCACAATAG | GTTACTTAAATGACCAT c.1320
P A A L A S P S A R V S T I G | Y L N D H p.440
. . . . . . g.1004120
GATGCTGTCACCAAGGCAATCCAAGAAGCTCGGCAAATGAAGGAGCAACTCCGACGGGAA c.1380
D A V T K A I Q E A R Q M K E Q L R R E p.460
. . . . . . g.1004180
CAACAGGTGCTTGATGGGAAGGTGGCTGTTGTGAATAGTCTGGGTCTCAATAACTGCCGA c.1440
Q Q V L D G K V A V V N S L G L N N C R p.480
| 15 . . . . . g.1021073
ACAGAAAAG | GAAAAAACAACACTGGAGAGTCTGACTCAGCAACTGGCAGTTAAACAGAAT c.1500
T E K | E K T T L E S L T Q Q L A V K Q N p.500
. . . . . | 16 g.1024064
GAAGAAGGAAAATTTAGCCATGCAATGATGGATTTCAATCTGAGTGGAGATTCTGATG | GA c.1560
E E G K F S H A M M D F N L S G D S D G | p.520
. . . . . . g.1024124
AGTGCTGGAGTCTCAGAGTCAAGAATTTATAGGGAATCCCGAGGGCGTGGTAGCAATGAA c.1620
S A G V S E S R I Y R E S R G R G S N E p.540
. . . . . . g.1024184
CCCCACATAAAGCGTCCAATGAATGCCTTCATGGTGTGGGCTAAAGATGAACGGAGAAAG c.1680
P H I K R P M N A F M V W A K D E R R K p.560
. . . . . | 17 . g.1030785
ATCCTTCAAGCCTTTCCTGACATGCACAACTCCAACATCAGCAAGATATTGG | GATCTCGC c.1740
I L Q A F P D M H N S N I S K I L G | S R p.580
. . . . . . g.1030845
TGGAAAGCTATGACAAACCTAGAGAAACAGCCATATTATGAGGAGCAAGCCCGTCTCAGC c.1800
W K A M T N L E K Q P Y Y E E Q A R L S p.600
. . . . . . g.1030905
AAGCAGCACCTGGAGAAGTACCCTGACTATAAGTACAAGCCCAGGCCAAAGCGCACCTGC c.1860
K Q H L E K Y P D Y K Y K P R P K R T C p.620
. . . . . . g.1030965
CTGGTGGATGGCAAAAAGCTGCGCATTGGTGAATACAAGGCAATCATGCGCAACAGGCGG c.1920
L V D G K K L R I G E Y K A I M R N R R p.640
. . | 18 . . . g.1032955
CAGGAAATGCGGCAGTACTTCAATGTTGG | GCAACAAGCACAGATCCCCATTGCCACTGCT c.1980
Q E M R Q Y F N V G | Q Q A Q I P I A T A p.660
. . . . . . g.1033015
GGTGTTGTGTACCCTGGAGCCATCGCCATGGCTGGGATGCCCTCCCCTCACCTGCCCTCG c.2040
G V V Y P G A I A M A G M P S P H L P S p.680
. . . . . . g.1033075
GAGCACTCAAGCGTGTCTAGCAGCCCAGAGCCTGGGATGCCTGTTATCCAGAGCACTTAC c.2100
E H S S V S S S P E P G M P V I Q S T Y p.700
. . . . . . g.1033135
GGTGTGAAAGGAGAGGAGCCACATATCAAAGAAGAGATACAGGCCGAGGACATCAATGGA c.2160
G V K G E E P H I K E E I Q A E D I N G p.720
. . . . . . g.1033195
GAAATTTATGATGAGTACGACGAGGAAGAGGATGATCCAGATGTAGATTATGGGAGTGAC c.2220
E I Y D E Y D E E E D D P D V D Y G S D p.740
. . . g.1033228
AGTGAAAACCATATTGCAGGACAAGCCAACTGA c.2253
S E N H I A G Q A N X p.750
. . . . . . g.1033288
taagggtcaaaagattgttgtgaccttaggacttaaagaagccctaactggttcatcctt c.*60
. . . . . . g.1033348
accagtggccaagcacattaactttctcatacactgactgttactttaactgttagtctt c.*120
. . . . . . g.1033408
aaatagttgggacatcagctgactaatagacctcagcctcaaaaggcttggaaagaaaaa c.*180
. . . . . . g.1033468
acaaatacaacaagcaaacaacaatatcaacaacaagagattgaaataagctatgggtaa c.*240
. . . . . . g.1033528
aataatgccagtaattcagctgctacatccaagcactgaagtcttacccgtcaacttttt c.*300
. . . . . . g.1033588
tttttttttaaataaactttatggctgtttgttctacaatgttctagaaattctcactca c.*360
. . . . . . g.1033648
ggtacacagtgccaacaagtggcttgtgaatgtgttttgttgttttgtgctacaattttt c.*420
. . . . . . g.1033708
aaaaagaaaaaagttttgttttgttttttggggtttctgggttttttccttttctttttc c.*480
. . . . . . g.1033768
tttcctttcattttttttctttgtaatgcacctgacagaaaaaaaagaaaaatgaatttc c.*540
. . . . . . g.1033828
tctttacttctctccaccttctccatctctctactttaaagatggaagtctgtgcatgag c.*600
. . . . . . g.1033888
gggaaagagggaaaaagagcctgtttttaacttccttgctatccaccacaaaataagcaa c.*660
. . . . . . g.1033948
ttattttctttagaggactttatctattgcacaccacactacatctttgagcaagtgcca c.*720
. . . . . . g.1034008
aatttgtactgaagtgttgaccaagttcattttttctctttactttttccttttccttct c.*780
. . . . . . g.1034068
taagttaggacagtgttaaatcttagacaatcccttgaaaaacctgaaataccagcagct c.*840
. . . . . . g.1034128
ggtgagatttgacttttttttttaatggaaactgtaggtgctgttctcaggtgaaaagag c.*900
. . . . . . g.1034188
agagagagagagagacataagaaatttagagaaaaatattttctgatcttggatttttgt c.*960
. . . . . . g.1034248
gtgtatgtatgtatgtgattatggtactaataataggaataacgttggaccattgtgagt c.*1020
. . . . . . g.1034308
taaacccacatctggggatgaaatcccacatcctcccaagtgactggtctagaaataatc c.*1080
. . . . . . g.1034368
ttgaccttgactttgcacttcaaatgacaacttaaccaagtatagggctcagaaattata c.*1140
. . . . . . g.1034428
tttttaaatgtctgattattattggatggatcaggtggccctgtgtaatagaggtgtgca c.*1200
. . . . . . g.1034488
tgtataacatggaagctactagcaaactgctcccagatgtcctttctccctggtcagttg c.*1260
. . . . . . g.1034548
gttccattaacgtttgctacttagtgatttttgtttttcctgttgatattttgagcaaaa c.*1320
. . . . . . g.1034608
caatcattgttttcattgaatatatttggccattttttcagacaaatagaattagcttat c.*1380
. . . . . . g.1034668
ttcttcaacattccatcctttcccgatcaggaaatgaaactgatgattttataaggtatt c.*1440
. . . . . . g.1034728
tttcacccctccatgaagtgaggtggaggcctttagcatttcagaagtgtgggccatatg c.*1500
. . . . . . g.1034788
tagttcatgccataaaaagtaggatttaattaaaagtcattgcagcccaataaaatggag c.*1560
. . . . . . g.1034848
cctggctgcacccagggatccttgccactgctcttcccttgctgtcagattaatccactg c.*1620
. . . . . . g.1034908
aagtccaactttggttcaagcagagtatttgcaaagagcaacaactgaatgtgatgggac c.*1680
. . . . . . g.1034968
tgcttatgtagattttgccagccaaatgccaaggcagttgtagggcctgtacaaataaat c.*1740
. . . . . . g.1035028
gcaaaatcatttcaagtcaattgccattatttgtattgaagtatcagatagatagtaaat c.*1800
. . . . . . g.1035088
actgcaactagtagcttgatgtgctatagttttcactccagtcatcattttcctatctca c.*1860
. . . . . . g.1035148
ccccccgaaacaccaccctaaagttggatttttacatataaataaaaaaagaatcccttt c.*1920
g.1035150
ta c.*1922
(downstream sequence)
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