(used for variant description)
(last modified February 3, 2016)
This file was created to facilitate the description of sequence variants on transcript NM_000346.3 in the SOX9 gene based on a coding DNA reference sequence following the HGVS recommendations.
The sequence was taken from NG_012490.1, covering SOX9 transcript NM_000346.3.
(upstream sequence)
. g.5012
ggagagccgaaa c.-361
. . . . . . g.5072
gcggagctcgaaactgactggaaacttcagtggcgcggagactcgccagtttcaaccccg c.-301
. . . . . . g.5132
gaaacttttctttgcaggaggagaagagaaggggtgcaagcgcccccacttttgctcttt c.-241
. . . . . . g.5192
ttcctcccctcctcctcctctccaattcgcctccccccacttggagcgggcagctgtgaa c.-181
. . . . . . g.5252
ctggccaccccgcgccttcctaagtgctcgccgcggtagccggccgacgcgccagcttcc c.-121
. . . . . . g.5312
ccgggagccgcttgctccgcatccgggcagccgaggggagaggagcccgcgcctcgagtc c.-61
. . . . . . g.5372
cccgagccgccgcggcttctcgcctttcccggccaccagccccctgccccgggcccgcgt c.-1
. . . . . . g.5432
ATGAATCTCCTGGACCCCTTCATGAAGATGACCGACGAGCAGGAGAAGGGCCTGTCCGGC c.60
M N L L D P F M K M T D E Q E K G L S G p.20
. . . . . . g.5492
GCCCCCAGCCCCACCATGTCCGAGGACTCCGCGGGCTCGCCCTGCCCGTCGGGCTCCGGC c.120
A P S P T M S E D S A G S P C P S G S G p.40
. . . . . . g.5552
TCGGACACCGAGAACACGCGGCCCCAGGAGAACACGTTCCCCAAGGGCGAGCCCGATCTG c.180
S D T E N T R P Q E N T F P K G E P D L p.60
. . . . . . g.5612
AAGAAGGAGAGCGAGGAGGACAAGTTCCCCGTGTGCATCCGCGAGGCGGTCAGCCAGGTG c.240
K K E S E E D K F P V C I R E A V S Q V p.80
. . . . . . g.5672
CTCAAAGGCTACGACTGGACGCTGGTGCCCATGCCGGTGCGCGTCAACGGCTCCAGCAAG c.300
L K G Y D W T L V P M P V R V N G S S K p.100
. . . . . . g.5732
AACAAGCCGCACGTCAAGCGGCCCATGAACGCCTTCATGGTGTGGGCGCAGGCGGCGCGC c.360
N K P H V K R P M N A F M V W A Q A A R p.120
. . . . . . g.5792
AGGAAGCTCGCGGACCAGTACCCGCACTTGCACAACGCCGAGCTCAGCAAGACGCTGGGC c.420
R K L A D Q Y P H L H N A E L S K T L G p.140
. | 02 . . . . . g.6748
AAGCTCTGGAG | ACTTCTGAACGAGAGCGAGAAGCGGCCCTTCGTGGAGGAGGCGGAGCGG c.480
K L W R | L L N E S E K R P F V E E A E R p.160
. . . . . . g.6808
CTGCGCGTGCAGCACAAGAAGGACCACCCGGATTACAAGTACCAGCCGCGGCGGAGGAAG c.540
L R V Q H K K D H P D Y K Y Q P R R R K p.180
. . . . . . g.6868
TCGGTGAAGAACGGGCAGGCGGAGGCAGAGGAGGCCACGGAGCAGACGCACATCTCCCCC c.600
S V K N G Q A E A E E A T E Q T H I S P p.200
. . . . . . g.6928
AACGCCATCTTCAAGGCGCTGCAGGCCGACTCGCCACACTCCTCCTCCGGCATGAGCGAG c.660
N A I F K A L Q A D S P H S S S G M S E p.220
. . | 03 . . . . g.7558
GTGCACTCCCCCGGCGAGCACTCGG | GGCAATCCCAGGGCCCACCGACCCCACCCACCACC c.720
V H S P G E H S G | Q S Q G P P T P P T T p.240
. . . . . . g.7618
CCCAAAACCGACGTGCAGCCGGGCAAGGCTGACCTGAAGCGAGAGGGGCGCCCCTTGCCA c.780
P K T D V Q P G K A D L K R E G R P L P p.260
. . . . . . g.7678
GAGGGGGGCAGACAGCCCCCTATCGACTTCCGCGACGTGGACATCGGCGAGCTGAGCAGC c.840
E G G R Q P P I D F R D V D I G E L S S p.280
. . . . . . g.7738
GACGTCATCTCCAACATCGAGACCTTCGATGTCAACGAGTTTGACCAGTACCTGCCGCCC c.900
D V I S N I E T F D V N E F D Q Y L P P p.300
. . . . . . g.7798
AACGGCCACCCGGGGGTGCCGGCCACGCACGGCCAGGTCACCTACACGGGCAGCTACGGC c.960
N G H P G V P A T H G Q V T Y T G S Y G p.320
. . . . . . g.7858
ATCAGCAGCACCGCGGCCACCCCGGCGAGCGCGGGCCACGTGTGGATGTCCAAGCAGCAG c.1020
I S S T A A T P A S A G H V W M S K Q Q p.340
. . . . . . g.7918
GCGCCGCCGCCACCCCCGCAGCAGCCCCCACAGGCCCCGCCGGCCCCGCAGGCGCCCCCG c.1080
A P P P P P Q Q P P Q A P P A P Q A P P p.360
. . . . . . g.7978
CAGCCGCAGGCGGCGCCCCCACAGCAGCCGGCGGCACCCCCGCAGCAGCCACAGGCGCAC c.1140
Q P Q A A P P Q Q P A A P P Q Q P Q A H p.380
. . . . . . g.8038
ACGCTGACCACGCTGAGCAGCGAGCCGGGCCAGTCCCAGCGAACGCACATCAAGACGGAG c.1200
T L T T L S S E P G Q S Q R T H I K T E p.400
. . . . . . g.8098
CAGCTGAGCCCCAGCCACTACAGCGAGCAGCAGCAGCACTCGCCCCAACAGATCGCCTAC c.1260
Q L S P S H Y S E Q Q Q H S P Q Q I A Y p.420
. . . . . . g.8158
AGCCCCTTCAACCTCCCACACTACAGCCCCTCCTACCCGCCCATCACCCGCTCACAGTAC c.1320
S P F N L P H Y S P S Y P P I T R S Q Y p.440
. . . . . . g.8218
GACTACACCGACCACCAGAACTCCAGCTCCTACTACAGCCACGCGGCAGGCCAGGGCACC c.1380
D Y T D H Q N S S S Y Y S H A A G Q G T p.460
. . . . . . g.8278
GGCCTCTACTCCACCTTCACCTACATGAACCCCGCTCAGCGCCCCATGTACACCCCCATC c.1440
G L Y S T F T Y M N P A Q R P M Y T P I p.480
. . . . . . g.8338
GCCGACACCTCTGGGGTCCCTTCCATCCCGCAGACCCACAGCCCCCAGCACTGGGAACAA c.1500
A D T S G V P S I P Q T H S P Q H W E Q p.500
. . . g.8368
CCCGTCTACACACAGCTCACTCGACCTTGA c.1530
P V Y T Q L T R P X p.509
. . . . . . g.8428
ggaggcctcccacgaagggcgaagatggccgagatgatcctaaaaataaccgaagaaaga c.*60
. . . . . . g.8488
gaggaccaaccagaattccctttggacatttgtgtttttttgtttttttattttgttttg c.*120
. . . . . . g.8548
ttttttcttcttcttcttcttccttaaagacatttaagctaaaggcaactcgtacccaaa c.*180
. . . . . . g.8608
tttccaagacacaaacatgacctatccaagcgcattacccacttgtggccaatcagtggc c.*240
. . . . . . g.8668
caggccaaccttggctaaatggagcagcgaaatcaacgagaaactggactttttaaaccc c.*300
. . . . . . g.8728
tcttcagagcaagcgtggaggatgatggagaatcgtgtgatcagtgtgctaaatctctct c.*360
. . . . . . g.8788
gcctgtttggactttgtaattatttttttagcagtaattaaagaaaaaagtcctctgtga c.*420
. . . . . . g.8848
ggaatattctctattttaaatatttttagtatgtactgtgtatgattcattaccattttg c.*480
. . . . . . g.8908
aggggatttatacatatttttagataaaattaaatgctcttatttttccaacagctaaac c.*540
. . . . . . g.8968
tactcttagttgaacagtgtgccctagcttttcttgcaaccagagtatttttgtacagat c.*600
. . . . . . g.9028
ttgctttctcttacaaaaagaaaaaaaaaatcctgttgtattaacatttaaaaacagaat c.*660
. . . . . . g.9088
tgtgttatgtgatcagttttgggggttaactttgcttaattcctcaggctttgcgattta c.*720
. . . . . . g.9148
aggaggagctgccttaaaaaaaaataaaggccttattttgcaattatgggagtaaacaat c.*780
. . . . . . g.9208
agtctagagaagcatttggtaagctttatcatatatatattttttaaagaagagaaaaac c.*840
. . . . . . g.9268
accttgagccttaaaacggtgctgctgggaaacatttgcactcttttagtgcatttcctc c.*900
. . . . . . g.9328
ctgcctttgcttgttcactgcagtcttaagaaagaggtaaaaggcaagcaaaggagatga c.*960
. . . . . . g.9388
aatctgttctgggaatgtttcagcagccaataagtgcccgagcacactgcccccggttgc c.*1020
. . . . . . g.9448
ctgcctgggccccatgtggaaggcagatgcctgctcgctctgtcacctgtgcctctcaga c.*1080
. . . . . . g.9508
acaccagcagttaaccttcaagacattccacttgctaaaattatttattttgtaaggaga c.*1140
. . . . . . g.9568
ggttttaattaaaacaaaaaaaaattcttttttttttttttttccaattttaccttcttt c.*1200
. . . . . . g.9628
aaaataggttgttggagctttcctcaaagggtatggtcatctgttgttaaattatgttct c.*1260
. . . . . . g.9688
taactgtaaccagtttttttttatttatctctttaatctttttttattattaaaagcaag c.*1320
. . . . . . g.9748
tttctttgtattcctcaccctagatttgtataaatgcctttttgtccatcccttttttct c.*1380
. . . . . . g.9808
ttgttgtttttgttgaaaacaaactggaaacttgtttctttttttgtataaatgagagat c.*1440
. . . . . . g.9868
tgcaaatgtagtgtatcactgagtcatttgcagtgttttctgccacagacctttgggctg c.*1500
. . . . . . g.9928
ccttatattgtgtgtgtgtgtgggtgtgtgtgtgttttgacacaaaaacaatgcaagcat c.*1560
. . . . . . g.9988
gtgtcatccatatttctctgcatcttctcttggagtgagggaggctacctggaggggatc c.*1620
. . . . . . g.10048
agcccactgacagaccttaatcttaattactgctgtggctagagagtttgaggattgctt c.*1680
. . . . . . g.10108
tttaaaaaagacagcaaacttttttttttatttaaaaaaagatatattaacagttttaga c.*1740
. . . . . . g.10168
agtcagtagaataaaatcttaaagcactcataatatggcatccttcaatttctgtataaa c.*1800
. . . . . . g.10228
agcagatctttttaaaaagatacttctgtaacttaagaaacctggcatttaaatcatatt c.*1860
. . . . . . g.10288
ttgtctttaggtaaaagctttggtttgtgttcgtgttttgtttgtttcacttgtttccct c.*1920
. . . . . . g.10348
cccagccccaaaccttttgttctctccgtgaaacttacctttccctttttctttctcttt c.*1980
. . . . . g.10401
tttttttttgtatattattgtttacaataaatatacattgcattaaaaagaaa c.*2033
(downstream sequence)
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