(used for variant description)
(last modified May 12, 2017)
This file was created to facilitate the description of sequence variants
on transcript NM_020451.2 in the SEPN1 gene based on a coding DNA
reference sequence following the
HGVS recommendations. The sequence was taken from NG_009930.1,
covering SEPN1 transcript NM_020451.2.
Exon 3 can be differentially spliced (see transcript NM_206926.1).
NOTE: SEPN1 is a selenoprotien, meaning Selenium
is incorporated as selenocysteine (U or
Sec) at a UGA codon, normally a termination
codon (here *127
and *462). The
recognition of UGA as a selenocysteine codon requires a secondary
structure called SECIS (selenocysteine insertion sequence) that is located
in the 3' UTR of the transcript.
Please note that introns are available by clicking on the exon numbers above the sequence.
(upstream sequence)
. . . . . g.5055
ccccgccccgctctttcgcttcccgggccgccggcagccgccgccagccgcagcc c.-1
. . . . . . g.5115
ATGGGCCGGGCCCGGCCGGGCCAACGCGGGCCGCCCAGCCCCGGCCCCGCCGCGCAGCCT c.60
M G R A R P G Q R G P P S P G P A A Q P p.20
. . . . . . g.5175
CCCGCGCCACCGCGCCGCCGCGCCCGTTCCCTGGCGCTGCTCGGAGCCCTGCTGGCCGCC c.120
P A P P R R R A R S L A L L G A L L A A p.40
. . . . . . g.5235
GCCGCTGCCGCCGCCGTCCGGGTCTGCGCCCGCCACGCCGAGGCCCAGGCGGCCGCGCGG c.180
A A A A A V R V C A R H A E A Q A A A R p.60
| 02 . . . . . . g.5924
CAG | GAACTGGCGCTGAAGACCCTGGGGACAGATGGCCTTTTTCTCTTTTCCTCCTTGGAC c.240
Q | E L A L K T L G T D G L F L F S S L D p.80
. . . . . . g.5984
ACTGACGGGGATATGTACATCAGCCCTGAGGAGTTCAAACCCATTGCTGAGAAGCTAACA c.300
T D G D M Y I S P E E F K P I A E K L T p.100
| 03 . . . . . . g.6899
G | GGTCTTGTTCTGTCACCCAGACTGGAGTGCAGTGGTGCAGTCACAGCTCACTGCAGCCT c.360
G | S C S V T Q T G V Q W C S H S S L Q P p.120
^ differentially spliced exon
. . . . | 04 . . g.10004
CAACTTCCCTGGCTCAATTGATCCTCCTGCCTCAGCCTCCTGA | GGTCAACTCCCGCGGCC c.420
Q L P W L N U S S C L S L L R | S T P A A 140
. . . . . . g.10043
AGCTGCGAGGAGGAGGAGTTGCCCCCTGACCCTAGCGAGGAGACGCTCACCATAGAAGCC c.480
S C E E E E L P P D P S E E T L T I E A p.160
. . . . . | 05. g.13407
CGATTCCAGCCTCTGCTCCCGGAGACCATGACCAAGAGCAAAGATGGCTTCCTAGGG | GTC c.540
R F Q P L L P E T M T K S K D G F L G | V p.180
. . . . . . g.13467
TCCCGCCTCGCCCTGTCCGGCCTCCGAAACTGGACAGCCGCCGCCTCACCAAGTGCAGTG c.600
S R L A L S G L R N W T A A A S P S A V p.200
. . . . . . g.13527
TTTGCCACCCGCCACTTCCAGCCCTTCCTTCCCCCGCCAGGCCAGGAGCTGGGTGAGCCC c.660
F A T R H F Q P F L P P P G Q E L G E P p.220
. . . . . . g.13587
TGGTGGATCATCCCCAGTGAGCTGAGCATGTTCACTGGCTACCTGTCCAACAACCGCTTC c.720
W W I I P S E L S M F T G Y L S N N R F p.240
. . | 06. . . . g.13883
TATCCACCGCCGCCCAAGGGCAAGGAG | GTCATCATCCACCGGCTCCTGAGCATGTTCCAC c.780
Y P P P P K G K E | V I I H R L L S M F H p.260
. . . . . . g.13943
CCTCGGCCCTTTGTGAAGACCCGCTTTGCCCCTCAGGGAGCTGTGGCCTGCCTGACTGCC c.840
P R P F V K T R F A P Q G A V A C L T A p.280
. . . | 07 . . . g.14535
ATCAGCGACTTCTACTACACTGTGATGTTCCG | GATCCATGCCGAGTTCCAGCTCAGTGAG c.900
I S D F Y Y T V M F R | I H A E F Q L S E p.300
. . . . . . g.14595
CCGCCCGACTTCCCCTTTTGGTTCTCCCCTGCTCAGTTCACCGGCCACATCATCCTCTCC c.960
P P D F P F W F S P A Q F T G H I I L S p.320
. . . . . | 08 . g.16288
AAAGACGCCACCCACGTCCGCGACTTCCGGCTCTTCGTGCCCAACCACAG | GTCTCTGAAT c.1020
K D A T H V R D F R L F V P N H R | S L N p.340
. . . . . . g.16348
GTGGACATGGAGTGGCTTTACGGGGCCAGTGAAAGCAGCAACATGGAGGTGGACATCGGC c.1080
V D M E W L Y G A S E S S N M E V D I G p.360
. | 09 . . . . . g.16563
TACATACCCCAG | ATGGAGCTGGAGGCCACGGGCCCCTCTGTGCCCTCCGTGATCCTGGAT c.1140
Y I P Q | M E L E A T G P S V P S V I L D p.380
. . . . . . g.16623
GAGGATGGCAGCATGATCGACAGCCACCTGCCTTCAGGGGAGCCCCTGCAGTTTGTGTTT c.1200
E D G S M I D S H L P S G E P L Q F V F p.400
. . . . . . g.16683
GAGGAGATCAAGTGGCAGCAGGAGCTGAGCTGGGAGGAGGCTGCCCGGCGCCTGGAGGTG c.1260
E E I K W Q Q E L S W E E A A R R L E V p.420
. . | 10 . . . . g.17550
GCCATGTACCCCTTCAAGAAG | GTCTCCTACTTGCCGTTCACTGAGGCCTTCGACCGAGCC c.1320
A M Y P F K K | V S Y L P F T E A F D R A p.440
. . . . . . g.17610
AAGGCTGAGAACAAGCTGGTGCACTCAATCCTGCTGTGGGGGGCCCTGGATGACCAGTCC c.1380
K A E N K L V H S I L L W G A L D D Q S p.460
| 11. . . . . . g.18758
TGCTGAG | GTTCAGGGCGGACTCTCCGGGAGACTGTCCTGGAAAGTTCGCCCATCCTCACC c.1440
C U G | S G R T L R E T V L E S S P I L T p.480
SRE (Sec redefinition element)
. . . . . . g.18818
CTGCTCAACGAGAGCTTCATCAGCACCTGGTCCCTGGTGAAGGAGCTGGAGGAACTGCAG c.1500
L L N E S F I S T W S L V K E L E E L Q p.500
| 12 . . . . . . g.18961
| AACAACCAGGAGAACTCGTCCCACCAGAAGCTGGCTGGCCTGCACCTGGAGAAGTACAGC c.1560
| N N Q E N S S H Q K L A G L H L E K Y S p.520
. . . . | 13 . . g.20390
TTCCCCGTGGAGATGATGATCTGCCTGCCCAATGGCACCGTG | GTCCATCACATCAATGCC c.1620
F P V E M M I C L P N G T V | V H H I N A p.540
. . . . . . g.20450
AACTACTTCTTGGACATCACCTCCGTGAAGCCCGAGGAAATCGAGAGCAATCTCTTCAGC c.1680
N Y F L D I T S V K P E E I E S N L F S p.560
. . . . . . g.20510
TTCTCATCCACCTTTGAAGACCCGTCCACGGCCACCTACATGCAGTTCCTGAAGGAGGGA c.1740
F S S T F E D P S T A T Y M Q F L K E G p.580
. . . g.20543
CTCCGGCGTGGCCTGCCCCTCCTCCAGCCCTAG c.1773
L R R G L P L L Q P * p.590
. . . . . . g.20603
agtgcctggacgggatctgatgcacaggcccccacgcctcagagccagagtggtcctcag c.*60
. . . . . . g.20663
cccatttcagactgcagatgccgcccactcccaccccactcctaggctgccttggagggt c.*120
. . . . . . g.20723
acaagatccactgagggtggccaccacagccttggctccatggtggcgggtagacaaggg c.*180
. . . . . . g.20783
atgcctgggctgactgggcagaggaacctctagctctgactgtcactcggctctccctac c.*240
. . . . . . g.20843
ccatttggctctggaagctgcttggcccccccagatcagggcctgggtgaactccctgga c.*300
. . . . . . g.20903
cctttcctagccagccgcacagtctaggcccttgtggggtgaagaatggagggaggagca c.*360
. . . . . . g.20963
ggctaggaagacggggccaccaccctctccttgctttcagcccttcccacaggaaacatc c.*420
. . . . . . g.21023
aagaagccccagccaggaggggccaggctgccaaggcggctcccctgtttatctagagcc c.*480
. . . . . . g.21083
ttcgttcctggccataccccggactgccctcctgtgcctgatgtccccagctggggtcag c.*540
. . . . . . g.21143
tctcaacaggagccagtcttctggagcctctgggcagaaccctccatcagagtggaaatc c.*600
. . . . . . g.21203
agacgggaccccctgcagcttccctgaccacgccactgaccagctatctggggaagttta c.*660
. . . . . . g.21263
ctgtgaaggggtttctgcctttagcaatggggttcactaagggggttcccgaggcccagg c.*720
. . . . . . g.21323
gccaaggcactcccaccgcctaccttagcacagggtctctgcaggactgcgggagccagc c.*780
. . . . . . g.21383
gctcctgccgcccctcttgcccctcagaccttgcatccacagaagcacaacccagccaaa c.*840
. . . . . . g.21443
caccacagccttctccagagccggcactgtcccggcaaccaggggtgccccaggctagct c.*900
. . . . . . g.21503
cttctacctctggggcaccacggactccccttggccactcttgggactttggtccacgtc c.*960
. . . . . . g.21563
ctgagccactgaccacggccagtctctctttttatatgtgcagaaaagtgtttttacaca c.*1020
. . . . . . g.21623
aactttctcatggtttgtaggtatttttttataaccccagtgctgaggagaaaggagggg c.*1080
. . . . . . g.21683
cagtggcttccccggcagcagccccatgatggctgaatccgaaatcctcgatgggtccag c.*1140
. . . . . . g.21743
cttgatgtctttgcagctgcacctatgggaagaagtagtcctctcttccttctcctcttc c.*1200
. . . . . . g.21803
agctttttaaaaacagtcctcagaggatccatgatccccagcactgtcccatcctccaca c.*1260
. . . . . . g.21863
aaggcccacaggcatgcctgtactctctttcattaaggtcttgaagtcaggctgccccct c.*1320
. . . . . . g.21923
ccccagcccccagttctctccccaccccctcaccccacccggggctcactcagcctggca c.*1380
. . . . . . g.21983
gaggaagaaggaaggcagacatctccgcagccactcctgggccttttatgtgccgagtta c.*1440
. . . . . . g.22043
ccccacttgccttgggcgtgtccactgagccttccccagccagtcttgttctcaattttg c.*1500
. . . . . . g.22103
ttttgttttgttttgagacggagtcttgctctgtcacccaggctggagtgctatggctcg c.*1560
. . . . . . g.22163
atcttggctcactgcaacctccacctcccaggttcaagcaattctcttgcctcagcctcc c.*1620
. . . . . . g.22223
cgagtagctgggattacaggtgcatgccaccatggctggctaatttttgtatttttagta c.*1680
. . . . . . g.22283
gagatggggtttcaccatattggtcaggctgatctggaacttctgacctcaggtgatcca c.*1740
. . . . . . g.22343
cctgcctcagcctcccaaagtgctgggattacaggcgtgagcaatcgtgcccagccttgt c.*1800
. . . . . . g.22403
tcttaattttgtatcatccagtcatcgctaatattacacgcaccttctcacttaatcctc c.*1860
. . . . . . g.22463
acgacaagcctgtgaggcagatgctcattgttcccatcttgatgaaacttgagtctcagg c.*1920
. . . . . . g.22523
gaagtgaagtgacttgcccagggtcactcaggtagagttgagattcaaacccacatgtgg c.*1980
. . . . . . g.22583
ctccaaagtctgcatctggatttgggggtgttttttggcatggcaccctcacctctctcc c.*2040
. . . . . . g.22643
ctgcctgttttccccaaagtggaaaggaaggcctttcaaaccagagtgtctcactcccct c.*2100
. . . . . . g.22703
ctgacctccagaccagatggggcatgagccagccagctcagccaggctccctgtgtcctg c.*2160
. . . . . . g.22763
ggaggaagtgtccccatcccccatgccccttatggggagggagggcgtctgatgctctct c.*2220
. . . . . . g.22823
ctctgcctccccccccatcctgtcaggcacaggtgacgggggcagcccatgcgagccctt c.*2280
. . . . . . g.22883
ctcctgctgctctgggagggccagttccacattgagccagcctggtcccatggaaaatga c.*2340
. . . . . . g.22943
tggcctgggctttctgaggccttatctgatgcctctgcagttcatgtcccccaccaggcc c.*2400
. . . . . . g.23003
tcgaggctcagggtgggagagggccccgggctgccctgtcactcctctaacacttccctc c.*2460
. . . . g.23047
ccctgtccccaacatgccctgtaataaaattagagaagactaac c.*2504
(downstream sequence)
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