Sequence
atgc intronic sequence ATGC exonic sequencegtttgtcctttgccatgcactcgttgtgtttactaagtcttgtttgagtttatacagttgagaaaaatgaatctttttttatgttgttgttgttgtgaatgtgcagATAAGTCCTTGTTTGGAGAGGAAGAATGGTATTTCTTTAGCCCGAGAGACAGGAAGTACCCGAATGGATTGAGGCCAAACAGGGCTGCAGCCTCAGGATA
Basic information
species | Glycine max |
transcript | GLYMA12G29360.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G29360.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S140_93V6.1 (Physcomitrella patens), 3'ss of exon 1
gtttgtcctttgcca--tgcactcgttgtgtttactaagtcttgtttgagtttatacagttgagaaaaatgaatctttttttatgttgttgttgttgtgaatgtgcagATAAGTCCTTGTTTGGAGAGGAAGAATGGTATTTCTTTAGCCCGAGAGACAGGAAGTACCCGAATGGATTGAGGCCAAACAGGGCTGCAGCCTCAGGATA
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-taagcttctcgcaaattgaacggaagttagttatttaaactt--ctgtgtccatgtgatcattaaacaccgaggttggagtataattaaaactttgc-----tgcagGAAAAGCAATATTCGGAGAGAGAGAATGGTATTTCTTCAGCCCACGAGACAGAAAGTACCCAAATGGAGCCAGACCCAACCGAGCAGCTGCCTCTGGGTA
upper sequence: GLYMA12G29360.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
gtttgtcctttgccatgcactcgttgtgtttactaagtcttgtttgagtttataca-gttgagaaaaatgaatctttttttatgttgttgttgttgtgaatgtgcagATAAGTCCTTGTTTGGAGAGGAAGAATGGTATTTCTTTAGCCCGAGAGACAGGAAGTACCCGAATGGATTGAGGCCAAACAGGGCTGCAGCCTCAGGATA
||| | | | | |||| | | || || | | || | ||| | | | | || | || | | || ||||| ||| | | |||||||| | ||| |||||||| || ||||| ||||||||||| ||||| |||||| | || ||| | |||||||| || |||||
------ttgttgaaacatagcagagcggcctactga-ttttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattctctactttgatttgcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
upper sequence: GLYMA12G29360.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S5_359V6.1 (Physcomitrella patens), 3'ss of exon 1
gtttgtcctttgccatgcactcgttgtgtttactaagtcttgtttga-gtttatacagttgagaaaaatgaatctttttttatgttgttgttgttgtgaatgtgcagATAAGTCCTTGTTTGGAGAGGAAGAATGGTATTTCTTTAGCCCGAGAGACAGGAAGTACCCGAATGGATTGAGGCCAAACAGGGCTGCAGCCTCAGGATA
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--tagtatcatctcacaaattgaaggcagcgcctaaactatccaacataacgattcagttgtaaaatactgagctttgagtaaaatgtcatgtttgc-----tgcagGAAAAGCAATTTTCGGAGAGAGGGAATGGTATTTCTTTAGTCCTAGAGATAGAAAGTACCCTAATGGAGCCAGGCCCAACAGAGCGGCCGCTTCAGGGTA
upper sequence: GLYMA12G29360.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S164_25V6.1 (Physcomitrella patens), 3'ss of exon 2
gtttgtcctttgccatgcactcgttgtgtttactaagtcttgtttgagtttatacagttgagaaaaatgaatctttttttatgttgttgttgttgtgaatgtgcagATAAGTCCTTGTTTGGAGAGGAAGAATGGTATTTCTTTAGCCCGAGAGACAGGAAGTACCCGAATGGATTGAGGCCAAACAGGGCTGCAGCCTCAGGATA
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atatgaca---acagtgcaatcatgtcgtaacata---cttgcaaaggatccccaaattgtagtctgtggcctaacaagtgatgcttaattgtgcaacgagtacagATAAGGCGTTGTTCGGAGAGAGAGAATGGTATTTCTTTTCTCCAAGGGACAGGAAGTACCCCAATGGCGCCAGGCCCAACAGAGCTGCCGCGAGTGGCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacagttgagaaaaatgaatctttttttatgttgttgttgttgtgaatgtgcagATAAGTCCTTGTTTGGAGAGGAAGAATGGTATTTCTTTAGCCCGAGAGACAGGAAGTACCCGAATGGATTGAGGCCAAACAGGGCTGCAGCCTCAGGATA
aaaaatgaatcttttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtcctttgccatgcactcgttgtgtttactaagtcttgtttgagtttatacagttgagaaaaatgaatctttttttatgttgttgttgttgtgaatgtgcagATAAGTCCTTGTTTGGAGAGGAAGAATGGTATTTCTTTAGCCCGAGAGACAGGAAGTACCCGAATGGATTGAGGCCAAACAGGGCTGCAGCCTCAGGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG