(used for variant description)
(last modified December 31, 2019)
This file was created to facilitate the description of sequence variants on transcript NM_007171.3 in the POMT1 gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_008896.1, covering POMT1 transcript variant-1 (NM_007171.3). Transcript variant-2 (NM_001077365.1) uses an alternative exonic splice site in exon 04. Transcript variant-3 (NM_001077366.1) skips exon 02 and uses an alternative exonic splice site in exon 04. Transcript variant-4 (NM_001136113.1) uses an alternative intronic (intron 01) splice donor site for exon 01 and an alternative exonic splice site in exon 04. Transcript variant-5 (NM_001136114.1) skips exons 02 and 03 and uses an alternative exonic splice site in exon 04.
Please note that introns are available by clicking on the exon numbers above the sequence.
(upstream sequence)
. . g.5022
acgcgcgctgctgcccgtctgg c.-181
. . . . . . g.5082
ccccgcaggctcggtgaatcgaacgttgagcagggcggtgggtggtgcggagtgccgagc c.-121
. . . . . . g.5142
ggcctcacccccaaccgtcggcccagtcggacggttccgaggcgttgccgggagccgggc c.-61
. . . | 02 . . g.6317
gcggctctgtgtggactcggagaaacgcgg | ggcgtctgcctgagcccgcttttctacaag c.-1
^ alternative splice site in intron 01
^ exon alternatively spliced (skipped)
. . . . . . g.6377
ATGTGGGGATTTTTGAAGCGCCCTGTAGTGGTGACGGCTGACATCAACTTGAGCCTTGTG c.60
M W G F L K R P V V V T A D I N L S L V p.20
. . . . . . g.6437
GCCCTGACTGGGATGGGGTTACTGAGCCGGCTGTGGCGACTCACCTACCCGCGGGCTGTG c.120
A L T G M G L L S R L W R L T Y P R A V p.40
| 03 . . . . . . g.8270
GT | TTTTGACGAAGTATATTATGGGCAGTACATCTCTTTTTACATGAAACAAATCTTCTTC c.180
V | F D E V Y Y G Q Y I S F Y M K Q I F F p.60
^ exon alternatively spliced (skipped)
. . . . | 04 . g.8512
TTGGATGACAGTGGGCCGCCATTTGGCCACATGGTGCTGGCCTTGGGAG | GTTATTTAGGA c.240
L D D S G P P F G H M V L A L G G | Y L G p.80
. . . . | 05 . . g.9486
GGATTCGATGGCAATTTTTTGTGGAACAGAATTGGAGCAG | AATACAGTAGCAACGTGCCT c.300
G F D G N F L W N R I G A E | Y S S N V P p.100
. . . . . . g.9546
GTGTGGTCCCTGCGCCTGCTGCCAGCACTCGCGGGGGCCTTGTCGGTCCCCATGGCCTAC c.360
V W S L R L L P A L A G A L S V P M A Y p.120
. . . . . . g.9606
CAGATAGTGTTGGAGCTCCACTTTTCTCATTGTGCCGCCATGGGAGCTGCTCTGTTGATG c.420
Q I V L E L H F S H C A A M G A A L L M p.140
| 06. . . . . . g.11062
CTTATCG | AGAATGCTCTCATCACTCAGTCAAGGCTAATGCTTTTGGAATCAGTGTTAATA c.480
L I E | N A L I T Q S R L M L L E S V L I p.160
. . . . . | 07 g.11842
TTTTTCAATCTATTGGCCGTGTTGTCCTACCTGAAGTTCTTCAACTGCCAAAAGCACAG | C c.540
F F N L L A V L S Y L K F F N C Q K H S | p.180
. . . . . . g.11902
CCTTTTTCTCTGAGCTGGTGGTTCTGGCTAACACTGACAGGGGTCGCTTGTTCCTGTGCA c.600
P F S L S W W F W L T L T G V A C S C A p.200
| 08 . . . . . . g.12056
GTGGG | CATCAAGTACATGGGTGTGTTCACGTACGTGCTCGTGCTGGGTGTTGCAGCTGTC c.660
V G | I K Y M G V F T Y V L V L G V A A V p.220
. . . / . . . g.12116
CATGCCTGGCACCTGCTTGGAGACCAGACTTTGTCCAAT / GTAGGTGCTGATGTCCAGTGC c.720
H A W H L L G D Q T L S N / V G A D V Q C p.240
alternative splice site ^
. . . . | 09 . . g.12373
TGCATGAGGCCGGCCTGTATGGGGCAGATGCGGATGTCACAGGGG | GTCTGTGTGTTCTGT c.780
C M R P A C M G Q M R M S Q G | V C V F C p.260
. . . . . . g.12433
CACTTGCTCGCCCGAGCAGTGGCTTTGCTGGTCATCCCGGTCGTCCTGTACTTACTGTTC c.840
H L L A R A V A L L V I P V V L Y L L F p.280
. . . . . . g.12493
TTCTACGTCCACTTGATTCTAGTCTTCCGCTCTGGGCCCCACGACCAAATCATGTCCAGT c.900
F Y V H L I L V F R S G P H D Q I M S S p.300
. . | 10 . . . . g.13474
GCCTTCCAGGCCAGCTTAGAG | GGAGGACTAGCTCGGATCACCCAGGGTCAGCCACTGGAG c.960
A F Q A S L E | G G L A R I T Q G Q P L E p.320
. . . . . . g.13534
GTGGCCTTTGGGTCCCAGGTCACTCTGAGGAACGTCTTTGGGAAACCTGTGCCCTGCTGG c.1020
V A F G S Q V T L R N V F G K P V P C W p.340
. . . | 11 . . . g.14167
CTTCATTCCCACCAGGACACCTACCCCATGAT | ATATGAGAACGGCCGAGGCAGCTCCCAC c.1080
L H S H Q D T Y P M I | Y E N G R G S S H p.360
. . . . . . g.14227
CAGCAACAGGTGACCTGTTACCCCTTCAAAGACGTCAATAACTGGTGGATTGTAAAGGAT c.1140
Q Q Q V T C Y P F K D V N N W W I V K D p.380
| 12 . . . . . g.15389
CCCAGGAG | GCACCAGCTGGTGGTGAGCAGCCCTCCGAGACCTGTGAGGCACGGGGACATG c.1200
P R R | H Q L V V S S P P R P V R H G D M p.400
. . . . | 13 . . g.17543
GTGCAGCTGGTCCACGGCATGACCACCCGCTCCCTGAACAC | GCATGATGTTGCAGCCCCC c.1260
V Q L V H G M T T R S L N T | H D V A A P p.420
. . . . . . g.17603
CTGAGCCCCCATTCACAGGAGGTCTCCTGCTACATTGACTATAACATCTCCATGCCCGCC c.1320
L S P H S Q E V S C Y I D Y N I S M P A p.440
. | 14 . . . . g.20585
CAGAACCTCTGGAGACTG | GAAATTGTGAACAGAGGATCTGACACAGACGTCTGGAAGACC c.1380
Q N L W R L | E I V N R G S D T D V W K T p.460
. . . . . | 15 . g.20944
ATCCTCTCAGAGGTCCGCTTTGTGCACGTGAACACTTCCGCTGTCTTAAAG | CTGAGCGGG c.1440
I L S E V R F V H V N T S A V L K | L S G p.480
. . . . . . g.21004
GCTCACCTCCCTGACTGGGGGTATCGGCAACTGGAGATCGTCGGGGAGAAGCTGTCCCGG c.1500
A H L P D W G Y R Q L E I V G E K L S R p.500
. . . . . | 16 . g.21495
GGCTACCACGGGAGCACGGTGTGGAACGTGGAGGAGCACCGATACGGCGCGA | GCCAGGAG c.1560
G Y H G S T V W N V E E H R Y G A S | Q E p.520
. . . . . . g.21555
CAGAGGGAGCGGGAACGGGAGCTGCACTCACCTGCGCAGGTGGACGTCAGCAGGAACCTC c.1620
Q R E R E R E L H S P A Q V D V S R N L p.540
. . . | 17 . . . g.22208
AGCTTCATGGCGAGATTCTCGGAGCTGCAG | TGGAGGATGCTGGCGCTGAGAAGTGATGAC c.1680
S F M A R F S E L Q | W R M L A L R S D D p.560
. . . . . . g.22268
TCGGAACACAAGTACAGCTCCAGCCCACTGGAGTGGGTCACCCTGGACACCAATATTGCC c.1740
S E H K Y S S S P L E W V T L D T N I A p.580
. . | 18 . . . . g.23480
TACTGGCTGCACCCCAGGACCAGC | GCTCAGATCCACCTACTTGGAAACATAGTGATCTGG c.1800
Y W L H P R T S | A Q I H L L G N I V I W p.600
. . . . . . g.23540
GTTTCGGGCAGCCTCGCTCTGGCCATCTACGCCCTGCTGTCCTTGTGGTACCTGCTCCGA c.1860
V S G S L A L A I Y A L L S L W Y L L R p.620
. . . | 19 . . . g.24174
CGGCGAAGAAATGTCCATGACCTCCCTCAGG | ATGCCTGGCTGCGCTGGGTGCTGGCTGGG c.1920
R R R N V H D L P Q D | A W L R W V L A G p.640
. . . . . . g.24234
GCGCTGTGTGCCGGTGGCTGGGCAGTGAACTACCTCCCGTTCTTCCTGATGGAGAAGACA c.1980
A L C A G G W A V N Y L P F F L M E K T p.660
. . . . . . g.24294
CTCTTCCTCTACCACTACCTGCCCGCACTCACCTTCCAAATCCTTCTGCTCCCTGTGGTC c.2040
L F L Y H Y L P A L T F Q I L L L P V V p.680
. . | 20 . . . g.25061
CTGCAGCACATCAGCGACCACCTGTGCAG | GTCCCAGCTCCAGAGGAGCATCTTCAGCGCC c.2100
L Q H I S D H L C R | S Q L Q R S I F S A p.700
. . . . . . g.25121
CTGGTGGTGGCCTGGTACTCCTCCGCGTGCCACGTGTCCAACACGCTGCGCCCACTCACC c.2160
L V V A W Y S S A C H V S N T L R P L T p.720
. . . . . . g.25181
TACGGGGACAAGTCACTCTCGCCACATGAACTCAAGGCCCTTCGCTGGAAAGACAGCTGG c.2220
Y G D K S L S P H E L K A L R W K D S W p.740
. . g.25205
GACATCTTGATCCGAAAACACTAG c.2244
D I L I R K H X p.747
. . . . . . g.25265
aacaagagtgtggcaaagaacacccgtgctggggtcgggatgaggttgaagggtcttggt c.*60
. . . . . . g.25325
caatgtacgtaatgagcagggtgggccccacgctgggaggacacgggctgggctgagcag c.*120
. . . . . . g.25385
ggcctctagtggaacacatgggggtctcattgaaaagctctctgatgagcacctcctttt c.*180
. . . . . . g.25445
gtgcaaagttaattttttctcgacaataaagatattccgtgtctttacccctgaactaag c.*240
. . . . . . g.25505
acacagggagtatttcagaggccagcgtaggagtcattgacaacaaaaagccgagaaccc c.*300
. . . . . . g.25565
agggccagcagtggagcctcagcagaccagggcctggtccttgctaactgctgcagggtg c.*360
. . . . . . g.25625
gagtttgatctggcagacccgatcctccttcatgaacacccagcaacctgagcaagtccc c.*420
. . . . . . g.25685
ggccctgccctcagcgagcccggcaggcgtcctgggacagctcagtgttggagggccacc c.*480
. . . . . . g.25745
tgaaccacgagccagggctggggcttgcatgtcattgtctatgacagcgtcaagactggc c.*540
. . . . . . g.25805
ccttggcaccgtgctgtgtggaaaccctcccctctgagactccactgagacgtggctgag c.*600
. . . . . . g.25865
tgaaatcttcctcgtcagtggtcaaggtgtgtcatccatacagctccatgcctttgtctt c.*660
. . . . g.25905
ttttaaatgtaattaaaaaaggaaccaactggcgtttgta c.*700
(downstream sequence)
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