(used for variant description)
(last modified December 31, 2019)
This file was created to facilitate the description of sequence variants on transcript NM_001243766.1 in the POMGNT1 gene based on a coding DNA reference sequence following the HGVS recommendations. The sequence was taken from NG_009205.2, covering POMGNT1 transcript variant-2 (NM_001243766.1). Transcript variant-1 (NM_017739.3) uses a different promoter/first exon (exon 1b) located in intron 1, an alternative splice site in intron 21 (exon 21b) and does not splice out intron 22.
Please note that introns are available by clicking on the exon numbers above the sequence.
(upstream sequence)
. . . . . g.5051
ctcagactgagggagaatcaattttgggggagaccacatctaatggataaa c.-601
. . . . . . g.5111
agagccacaggattacaaaagggtggaatagttgttacaagaaggtcacatcatcctggc c.-541
. . . . . . g.5171
actgctcccagaaccagtgggcctcgaagcccagcttggcactctcatcctctggtgact c.-481
. . . . . . g.5231
caggtggtccaccttgaagcctctcccctgggggcttccacacagctctcaagctcccta c.-421
. . . . . . g.5291
gcctggtggctgccacatccacctcagtcctggccctctctccaccagctataacttttg c.-361
. . . . . . g.5351
cccagtccatctcggaacgtggagccccaggtgggccctgttcatccagctcgctggggg c.-301
. . . . . . g.5411
ccactgtgtccaggaagctgccaatagagacactgtccagccggtcggtggtgctggtgt c.-241
. . . . . . g.5471
ctggcaggctgtcccagctgcctcgccttgagcggcctgggctcccgcctgtcaggctat c.-181
. . . . . . g.5531
attgactgctggtgaggctgctgcaatgactggtcaacgtcccccgctcctccaacagcc c.-121
. . . . . . g.5591
agcgcactgcctcgatgccctcattcaaggtcaccagctgctgcaggatcttcacatcga c.-61
. | 02 . . . . g.27484
tggctcgcag | attcctgaagtcatgggctggccaggacattggtgacccgccaatccggt c.-1
^ alternative promoter/first exon 1b
. . . . . . g.27544
ATGGACGACTGGAAGCCCAGCCCCCTCATCAAGCCCTTTGGGGCTCGGAAGAAGCGGAGC c.60
M D D W K P S P L I K P F G A R K K R S p.20
. . . . . . g.27604
TGGTACCTTACCTGGAAGTATAAACTGACAAACCAGCGGGCCCTGCGGAGATTCTGTCAG c.120
W Y L T W K Y K L T N Q R A L R R F C Q p.40
| 03 . . . . . . g.28281
| ACAGGGGCCGTGCTTTTCCTGCTGGTGACTGTCATTGTCAATATCAAGTTGATCCTGGAC c.180
| T G A V L F L L V T V I V N I K L I L D p.60
. . . . . | 04 . g.28461
ACTCGGCGAGCCATCAGTGAAGCCAATGAAGACCCAGAGCCAGAGCAAGACTATG | ATGAG c.240
T R R A I S E A N E D P E P E Q D Y D | E p.80
. . . . . . g.28521
GCCCTAGGCCGCCTGGAGCCCCCACGGCGCAGAGGCAGTGGTCCCCGGCGGGTCCTGGAC c.300
A L G R L E P P R R R G S G P R R V L D p.100
. . . . . | 05 . g.29234
GTAGAGGTGTATTCAAGTCGCAGCAAAGTATATGTGGCAGTGGATGGCACCACG | GTGCTG c.360
V E V Y S S R S K V Y V A V D G T T | V L p.120
. . . . . . g.29294
GAGGATGAGGCCCGGGAGCAGGGCCGGGGCATCCATGTCATTGTCCTCAACCAGGCCACG c.420
E D E A R E Q G R G I H V I V L N Q A T p.140
| 06 . . . . . . g.29441
| GGCCACGTGATGGCAAAACGTGTGTTTGACACGTACTCACCTCATGAGGATGAGGCCATG c.480
| G H V M A K R V F D T Y S P H E D E A M p.160
. . . . . | 07 . g.30350
GTGCTATTCCTCAACATGGTAGCGCCCGGCCGAGTGCTCATCTGCACTGTCAAG | GATGAG c.540
V L F L N M V A P G R V L I C T V K | D E p.180
. . . . . . g.30410
GGCTCCTTCCACCTCAAGGACACAGCCAAGGCTCTGCTGAGGAGCCTGGGCAGCCAGGCT c.600
G S F H L K D T A K A L L R S L G S Q A p.200
. . . . . | 08 . g.30662
GGCCCTGCCCTGGGCTGGAGGGACACATGGGCCTTCGTGGGACGAAAAGGAG | GTCCTGTC c.660
G P A L G W R D T W A F V G R K G G | P V p.220
. . . . . . g.30722
TTCGGGGAGAAACATTCTAAATCACCTGCCCTCTCTTCCTGGGGGGACCCAGTCCTGCTG c.720
F G E K H S K S P A L S S W G D P V L L p.240
. . . | 09 . . . g.30933
AAGACAGATGTGCCATTGAGCTCAGCAGAAG | AGGCAGAGTGCCACTGGGCAGACACAGAG c.780
K T D V P L S S A E E | A E C H W A D T E p.260
. . . . . . g.30993
CTGAACCGTCGCCGCCGGCGCTTCTGCAGCAAAGTTGAGGGCTATGGAAGTGTATGCAGC c.840
L N R R R R R F C S K V E G Y G S V C S p.280
. . . | 10 . . g.31401
TGCAAGGACCCCACACCCATCGAGTTCAGCCCTGACCCA | CTCCCAGACAACAAGGTCCTC c.900
C K D P T P I E F S P D P | L P D N K V L p.300
. . . . . | 11 . g.31676
AATGTGCCTGTGGCTGTCATTGCAGGGAACCGACCCAATTACCTGTACAG | GATGCTGCGC c.960
N V P V A V I A G N R P N Y L Y R | M L R p.320
. . . . . . g.31736
TCTCTGCTTTCAGCCCAGGGGGTGTCTCCTCAGATGATAACAGTTTTCATTGACGGCTAC c.1020
S L L S A Q G V S P Q M I T V F I D G Y p.340
| 12 . . . . . . g.31971
TATGAG | GAACCCATGGATGTGGTGGCACTGTTTGGTCTGAGGGGCATCCAGCATACTCCC c.1080
Y E | E P M D V V A L F G L R G I Q H T P p.360
. . . | 13 . . . g.32120
ATCAGCATCAAGAATGCCCGCGTGTCTCAG | CACTACAAGGCCAGCCTCACTGCCACTTTC c.1140
I S I K N A R V S Q | H Y K A S L T A T F p.380
. | 14 . . . . . g.32395
AACCTGTTTCCG | GAGGCCAAGTTTGCTGTGGTTCTGGAAGAGGACCTGGACATTGCTGTG c.1200
N L F P | E A K F A V V L E E D L D I A V p.400
. | 15 . . . . . g.32764
GATTTTTTCAG | TTTCCTGAGCCAATCCATCCACCTACTGGAGGAGGATGACAGCCTGTAC c.1260
D F F S | F L S Q S I H L L E E D D S L Y p.420
. . | 16 . . . . g.32905
TGCATCTCTGCCTGGAATGACCAG | GGGTATGAACACACGGCTGAGGACCCAGCACTACTG c.1320
C I S A W N D Q | G Y E H T A E D P A L L p.440
. . . . . . g.32965
TACCGTGTGGAGACCATGCCTGGGCTGGGCTGGGTGCTCAGGAGGTCCTTGTACAAGGAG c.1380
Y R V E T M P G L G W V L R R S L Y K E p.460
. . . | 17 . . . g.33109
GAGCTTGAGCCCAAGTGGCCTACACCGGAAAAG | CTCTGGGATTGGGACATGTGGATGCGG c.1440
E L E P K W P T P E K | L W D W D M W M R p.480
. . . . . . g.33169
ATGCCTGAACAACGCCGGGGCCGAGAGTGCATCATCCCTGACGTTTCCCGATCCTACCAC c.1500
M P E Q R R G R E C I I P D V S R S Y H p.500
. . . | 18 . . g.34542
TTTGGCATCGTCGGCCTCAACATGAATGGCTACTTTCAC | GAGGCCTACTTCAAGAAGCAC c.1560
F G I V G L N M N G Y F H | E A Y F K K H p.520
. . . . | 19 . . g.34804
AAGTTCAACACGGTTCCAGGTGTCCAGCTCAGGAATGTGGACAG | TCTGAAGAAAGAAGCT c.1620
K F N T V P G V Q L R N V D S | L K K E A p.540
. . | 20 . . . g.35347
TATGAAGTGGAAGTTCACAGGCTGCTCAG | TGAGGCTGAGGTTCTGGACCACAGCAAGAAC c.1680
Y E V E V H R L L S | E A E V L D H S K N p.560
. . . . . . g.35407
CCTTGTGAAGACTCTTTCCTGCCAGACACAGAGGGCCACACCTACGTGGCCTTTATTCGA c.1740
P C E D S F L P D T E G H T Y V A F I R p.580
. . . . | 21 . . g.35753
ATGGAGAAAGATGATGACTTCACCACCTGGACCCAGCTTGCCAAG | TGCCTCCATATCTGG c.1800
M E K D D D F T T W T Q L A K | C L H I W p.600
. . . . . . g.35813
GACCTGGATGTGCGTGGCAACCATCGGGGCCTGTGGAGATTGTTTCGGAAGAAGAACCAC c.1860
D L D V R G N H R G L W R L F R K K N H p.620
| 22 . . . . . g.35999
TTCCTGGTG | AGTGAAGAAGCCACCCTCAGTCACCCCAATTTTCCTGGAGCCACCCCCAAA c.1920
F L V | S E E A T L S H P N F P G A T P K p.640
^ alternatively spliced exon 21b
V K K P P S V T P I F L E P P P K p.623+26
alternative reading frame transcript variant-1
. . . . . . g.36059
GGAGGAGGGAGCCCCAGGAGCCCCAGAACAGACATGAGACCTCCTCCAGGACCCTGCGGG c.1980
G G G S P R S P R T D M R P P P G P C G p.660
E E G A P G A P E Q T *
| 23 . . . . . . g.36380
GCTGG | GCCTGGCTCAGAATCTAACCTATTTATTGACTGTCCTGAGGGCCTTGAAAACAGG c.2040
A G | P G S E S N L F I D C P E G L E N R p.680
^ intron 22 not spliced in transcript variant-1
. . . . . . g.36440
CCGAACCTGGAGGGCCTGGATTTCTTTTTGGGCTGGAATGCTGCCCTGAGGGTGGGGCTG c.2100
P N L E G L D F F L G W N A A L R V G L p.700
. . . . . . g.36500
GCTCTTACTCAGGAAACTGCTGTGCCCAACCCATGGACAGGCCCAGCTGGGGCCCACATG c.2160
A L T Q E T A V P N P W T G P A G A H M p.720
. . . . . . g.36560
CTGACACAGACTCACTCAGAGACCCTTAGACACTGGACCAGGCCTCCTCTCAGCCTTCTC c.2220
L T Q T H S E T L R H W T R P P L S L L p.740
. . g.36587
TTTGTCCAGATTTCCAAAGCTGGATAA c.2247
F V Q I S K A G X p.748
. . . g.36625
gttggtcattgattaaaaaaggagaagccctctgggga c.*38
(downstream sequence)
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