(used for variant description)
(last modified November 13, 2020)
This file was created to facilitate the description of sequence variants on transcript NM_001851.4 in the COL9A1 gene based on a coding DNA reference sequence following the HGVS recommendations.
The sequence was taken from NG_011654.1, covering COL9A1 transcript NM_001851.4.
(upstream sequence)
. . . g.5039
cctttgcttttagccctcaccgggggcaggagggaccaa c.-121
. . . . . . g.5099
ggctgggcccagaacacatagtcctagggtaacagtgaaggggtcgtgaggggacagtga c.-61
. . . . . . g.5159
ctcccttccaaccccttcttcatagggactgttggcaaacaaagaaaatcaactgggaaa c.-1
. | 02 . . . . . g.6055
ATGAAGACCTGCTG | GAAAATTCCAGTTTTCTTCTTTGTGTGCAGTTTCCTGGAACCCTGG c.60
M K T C W | K I P V F F F V C S F L E P W p.20
. . | 03 . . . g.7729
GCATCTGCAGCTGTCAAGCGTCGCCCCA | GATTCCCTGTCAATTCCAATTCTAATGGTGGA c.120
A S A A V K R R P R | F P V N S N S N G G p.40
. . . . | 04 . . g.7922
AATGAACTCTGTCCAAAGATCAGGATTGGCCAAGATGACTTACCAG | GGTTTGATCTGATC c.180
N E L C P K I R I G Q D D L P G | F D L I p.60
. . . . . . g.7982
TCTCAGTTCCAGGTAGATAAAGCAGCATCTAGAAGAGCTATCCAGAGAGTAGTGGGATCA c.240
S Q F Q V D K A A S R R A I Q R V V G S p.80
. . . . . | 05 g.13521
GCTACATTGCAGGTGGCTTACAAGTTGGGAAATAATGTAGACTTCAGGATTCCAACTAG | G c.300
A T L Q V A Y K L G N N V D F R I P T R | p.100
. . . . . . g.13581
AATTTATATCCCAGTGGACTGCCTGAAGAATACTCCTTCTTGACGACGTTTCGAATGACT c.360
N L Y P S G L P E E Y S F L T T F R M T p.120
. . . . . . g.13641
GGAAGCACTCTCAAAAAGAACTGGAACATTTGGCAGATTCAGGATTCCTCTGGGAAGGAG c.420
G S T L K K N W N I W Q I Q D S S G K E p.140
. . . . . . g.13701
CAAGTTGGCATAAAGATTAATGGCCAAACACAATCTGTTGTATTTTCATACAAGGGACTG c.480
Q V G I K I N G Q T Q S V V F S Y K G L p.160
. . . . . . g.13761
GATGGAAGTCTCCAAACAGCAGCCTTTTCGAATTTGTCCTCCTTGTTTGATTCCCAGTGG c.540
D G S L Q T A A F S N L S S L F D S Q W p.180
. . . . . . g.13821
CATAAGATCATGATTGGCGTGGAGAGGAGTAGTGCTACTCTTTTTGTTGACTGCAACAGG c.600
H K I M I G V E R S S A T L F V D C N R p.200
. . . . . . g.13881
ATTGAATCTTTACCTATAAAGCCAAGAGGCCCAATTGACATTGATGGCTTTGCTGTGCTG c.660
I E S L P I K P R G P I D I D G F A V L p.220
. . . | 06 . . . g.24287
GGAAAACTTGCAGATAATCCTCAAGTTTCTGTTCCA | TTTGAACTTCAATGGATGCTGATC c.720
G K L A D N P Q V S V P | F E L Q W M L I p.240
. . . . . . g.24347
CATTGTGACCCCCTGCGGCCCAGGAGAGAAACTTGCCATGAGCTGCCAGCCAGAATAACG c.780
H C D P L R P R R E T C H E L P A R I T p.260
| 07 . . | 08 . . . . g.26658
| CCCAGCCAGACCACCGACGAG | AGAGGTCCCCCGGGTGAGCAGGGTCCTCCCGGGCCTCCG c.840
| P S Q T T D E | R G P P G E Q G P P G P P p.280
. . . | 09 . . . g.27068
GGCCCCCCTGGAGTTCCAGGCATCGATGGCATCGAC | GGTGACCGAGGTCCTAAGGGCCCC c.900
G P P G V P G I D G I D | G D R G P K G P p.300
. | 10 . . . . . g.27257
CCGGGCCCCCCG | GGTCCTGCAGGTGAACCGGGAAAGCCAGGAGCTCCAGGCAAGCCTGGC c.960
P G P P | G P A G E P G K P G A P G K P G p.320
. | 11 . . . . . g.33356
ACACCTGGCGCTGAT | GGATTAACAGGACCTGATGGATCCCCTGGCTCCATTGGGTCAAAG c.1020
T P G A D | G L T G P D G S P G S I G S K p.340
| 12 . . . | 13 . . g.36010
GGACAAAAA | GGAGAACCTGGTGTGCCTGGATCGCGTGGATTTCCA | GGCCGTGGTATTCCT c.1080
G Q K | G E P G V P G S R G F P | G R G I P p.360
| 14 . . . . . g.36426
GGACCCCCT | GGTCCTCCTGGGACAGCAGGACTCCCTGGAGAGCTTGGCCGTGTAGGACCT c.1140
G P P | G P P G T A G L P G E L G R V G P p.380
| 15 . . . . . | 16. g.38421
GTT | GGTGACCCTGGGAGAAGAGGACCACCTGGCCCCCCTGGCCCCCCAGGACCCAGA | GGA c.1200
V | G D P G R R G P P G P P G P P G P R | G p.400
. . . | 17 . . . g.39253
ACAATTGGCTTTCATGATGGAGATCCATTG | TGTCCCAATGCCTGTCCACCAGGTCGCTCA c.1260
T I G F H D G D P L | C P N A C P P G R S p.420
. . | 18. . . . g.41346
GGATATCCAGGCCTACCAGGCATGAGG | GGTCATAAAGGGGCTAAAGGAGAAATTGGTGAA c.1320
G Y P G L P G M R | G H K G A K G E I G E p.440
. . | 19 . . . . g.44825
CCAGGAAGACAAGGACACAAG | GGTGAAGAAGGTGACCAGGGAGAACTCGGAGAAGTTGGA c.1380
P G R Q G H K | G E E G D Q G E L G E V G p.460
. | 20 . . . . . g.47418
GCTCAAGGACCTCCA | GGAGCCCAGGGTTTGCGAGGCATCACCGGCATAGTTGGGGACAAA c.1440
A Q G P P | G A Q G L R G I T G I V G D K p.480
| 21 . . . . . g.51313
GGGGAAAAA | GGTGCTCGGGGCTTAGATGGTGAACCTGGGCCTCAGGGTCTTCCTGGTGCA c.1500
G E K | G A R G L D G E P G P Q G L P G A p.500
| 22 . . . . . | 23. g.52883
CCT | GGTGATCAAGGACAGCGAGGACCTCCAGGAGAAGCAGGTCCCAAAGGAGATAGA | GGG c.1560
P | G D Q G Q R G P P G E A G P K G D R | G p.520
. . . . . | 24 . g.53076
GCTGAAGGTGCTAGAGGAATTCCTGGTCTCCCTGGGCCCAAAGGAGACACG | GGTTTGCCA c.1620
A E G A R G I P G L P G P K G D T | G L P p.540
. . . . | 25 . . g.53569
GGTGTGGATGGCCGTGATGGGATCCCTGGAATGCCTGGAACAAAG | GGTGAACCAGGAAAA c.1680
G V D G R D G I P G M P G T K | G E P G K p.560
. . . | 26 . . g.54675
CCTGGGCCTCCTGGTGATGCAGGATTGCAGGGGTTACCA | GGTGTACCTGGAATTCCTGGT c.1740
P G P P G D A G L Q G L P | G V P G I P G p.580
. . | 27 . . . . g.55804
GCAAAGGGTGTTGCTGGTGAAAAG | GGTAGCACAGGTGCTCCAGGGAAGCCTGGTCAGATG c.1800
A K G V A G E K | G S T G A P G K P G Q M p.600
. | 28 . . . . g.55952
GGAAATTCAGGCAAACCG | GGCCAACAGGGGCCTCCAGGAGAGGTGGGACCCCGAGGACCC c.1860
G N S G K P | G Q Q G P P G E V G P R G P p.620
. | 29 . . . . . g.65416
CAGGGGCTTCCT | GGCAGTAGAGGAGAATTAGGACCAGTGGGATCCCCAGGCCTACCAGGT c.1920
Q G L P | G S R G E L G P V G S P G L P G p.640
| 30 . . . . . . g.66102
AAACTG | GGTTCTCTGGGTAGCCCTGGCCTCCCTGGCTTGCCTGGGCCCCCTGGACTTCCT c.1980
K L | G S L G S P G L P G L P G P P G L P p.660
. | 31 . . . | 32 . g.67356
GGAATGAAAGGTGACAGG | GGTGTAGTCGGTGAACCGGGTCCAAAGGGTGAACAG | GGTGCC c.2040
G M K G D R | G V V G E P G P K G E Q | G A p.680
. . . | 33 . . g.68818
TCTGGTGAAGAAGGTGAAGCAGGAGAAAGGGGGGAACTT | GGAGATATAGGATTACCTGGC c.2100
S G E E G E A G E R G E L | G D I G L P G p.700
. | 34 . . . . . g.73191
CCAAAGGGATCT | GCAGGTAATCCTGGGGAACCTGGCTTGAGAGGGCCTGAGGGAAGTCGG c.2160
P K G S | A G N P G E P G L R G P E G S R p.720
. . . . . . g.73251
GGGCTTCCTGGAGTGGAAGGACCAAGAGGACCACCTGGACCCCGGGGTGTGCAGGGAGAA c.2220
G L P G V E G P R G P P G P R G V Q G E p.740
. . . | 35 . . g.73511
CAGGGTGCCACCGGCCTGCCTGGTGTCCAGGGCCCTCCG | GGTAGAGCACCGACAGATCAG c.2280
Q G A T G L P G V Q G P P | G R A P T D Q p.760
. . . | 36 . . . g.75338
CACATTAAGCAGGTTTGCATGAGAGTCATACAAG | AACATTTTGCTGAGATGGCTGCCAGT c.2340
H I K Q V C M R V I Q E | H F A E M A A S p.780
. . . . . . g.75398
CTTAAGCGTCCAGACTCAGGTGCCACTGGGCTTCCTGGAAGGCCTGGCCCTCCTGGTCCC c.2400
L K R P D S G A T G L P G R P G P P G P p.800
. . . . . . g.75458
CCCGGCCCTCCTGGAGAGAATGGTTTCCCAGGCCAGATGGGAATTCGTGGCCTTCCGGGC c.2460
P G P P G E N G F P G Q M G I R G L P G p.820
. . . . | 37 . . g.82091
ATTAAGGGGCCCCCTGGTGCTCTTGGTTTGAGGGGACCTAAAG | GTGACTTGGGAGAAAAG c.2520
I K G P P G A L G L R G P K G | D L G E K p.840
. . . . . . g.82151
GGGGAGCGTGGCCCTCCAGGAAGAGGTCCCAACGGTTTGCCTGGAGCTATAGGTCTCCCA c.2580
G E R G P P G R G P N G L P G A I G L P p.860
| 38 . . . . . . g.91061
G | GTGACCCAGGCCCTGCCAGCTATGGCAGAAATGGCCGAGACGGTGAGCGAGGCCCCCCA c.2640
G | D P G P A S Y G R N G R D G E R G P P p.880
. . . . . . g.91121
GGGGTGGCAGGAATTCCTGGAGTGCCTGGACCCCCGGGACCTCCTGGGCTTCCCGGTTTC c.2700
G V A G I P G V P G P P G P P G L P G F p.900
. . . . . . g.91181
TGTGAGCCAGCCTCCTGCACCATGCAGGCTGGTCAGCGAGCATTTAACAAAGGGCCTGAC c.2760
C E P A S C T M Q A G Q R A F N K G P D p.920
g.91187
CCTTGA c.2766
P X p.921
. . . . . . g.91247
aaggcttactgctgcatggctgtctgcatgaaccacgcctggtgaaggagcctgggtgag c.*60
. . . . . . g.91307
aaacaccatccaaagctggggcaaagatgattaccttcagcatgattacaatgtattacc c.*120
. . . . . . g.91367
ttcagtatgattacagaagtcctacttgacaatcacatatagaagaacggtgctattcag c.*180
. . . . . . g.91427
taagttctctttcctttcccttggagggaagacagcagagtcatcagttaaaaaaaaaaa c.*240
. . . . . . g.91487
aagaaaaccaaacacctcccttgaataaatttatactcctgttcccaggatcttgagctt c.*300
. . . . . . g.91547
tagtgtgctatacctatgtgtcttatcgtgggccactgtgccaataaacaaaaacaactg c.*360
. . . . . . g.91607
tttggtttacctcagttgcagtagttattttcatttagaagttgttctcagattattgtt c.*420
. . . . . . g.91667
tcagttatatagaggattactagactagttatgaagaaaccccactacattcaatggaat c.*480
. . . . . . g.91727
tggtgcttaaaatctcatcgatgtgctgtctctggagtgataagaaagggctacatctcc c.*540
. . . . . . g.91787
cgaaatgatttctttacgtcatgtattggtttccttcttcaccttgaacttttgttgaac c.*600
. . . . . . g.91847
tgtatgtactttaccccaaacctgttaatattttgagcgcttctatgtgaaagcaaagaa c.*660
. . . . . . g.91907
ataattttaatactctggcattcataaattttattgatgagattatttattttaaaggtt c.*720
. . . . . . g.91967
tgaggtaacatctctggttgtaccaaagaagaaataaatatggtttcttaatctcttgca c.*780
. . . . . . g.92027
tgttttcttataaataatcatgttcaatgaaaagaagttactgagcttatttagatacat c.*840
. g.92044
taaacattacttaacta c.*857
(downstream sequence)
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