Sequence
atgc intronic sequence ATGC exonic sequencegtgaatttcaatcgaatttgaatttgaactttactcaagtgccatatcactgtttttgttgatgtagGCTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAGCAGATTCGTTTGAAGATTTTTTCGCCCAATGTTCTCGACATTACGCTTGTGG
Basic information
species | Glycine max |
transcript | GLYMA07G30150.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G30150.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 1
--------------------------------gtgaatttcaa-tcgaatttgaatttgaactttactcaagtgccatatcactgtttttgttgatgtagGCTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAGCAGATTCGTTTGAAGATTTTTTCGCCCAATGTTCTCGACATTACGCTTGTGG
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tgtttggtattttgtttcacttcttttctttagttagtgtgggcttgagttgccattagtgctccacagaccattgttaaaagactctgcatctatgcagGCAGAAACAGACCGAGAGGCAGGTGGTAACAAAGGTGTATCGGATAGGCAGATACGATTGAAGATTTTTTCTCCAAATGTTCTTAACATTACTTTGGTTG
upper sequence: GLYMA07G30150.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 1
---------------------------gtgaatttcaatcgaatttgaa--tttgaactttact--caagtgccatatcactgtttttgttgatgt--agGCTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAGCAGATTCGTTTGAAGATTTTTTCGCCCAATGTTCTCGACATTACGCTTGTGG
|| | | | | || || |||||| | | | || | | | ||| | || | |||||||||| |||||||||||||||| ||||||||||| || ||||||||||||||||| ||||| || ||||| ||||| || || || || || ||||
ttatttttatcatctcaagctttgcatgtataccaaagtaatacttaaaactttgaagatagtttccccccccctcaaaattctttccaatcatcttcagGCTGAGACAGATAGGGAAGCTGGAGAAAACAAAGGTGTTTCAGATAAGCAGATTCGTTTAAAGATATTCTCGCCAAATGTCCTTGATATCACACTAGTGG
upper sequence: GLYMA07G30150.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S82_15V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------------------------------------------------------------------------------------------------gtgaatttcaatcg----aatttgaatttgaactttactcaagtgccatatcactgtttttg-----ttgatg--tagGCTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAGCAGATTCGTTTGAAGATTTTTTCGCCCAATGTTCTCGACATTACGCTTGTGG
| ||||| | | || || | || ||| || || | || |||| | ||| | ||| ||||| || |||| ||| || ||||| | ||||| |||||||||||||||||||||||||| || |||| | |||||||| | || |
gtacagctctgtgacaaaactttattcctaatctccgaaatttgcttcattctaactccagagaaaatcaattatgcctccttagcagaagatacggttagcatccaattccaaccttcccacgttcaactgtcctacttatgatctaaatttttctgtcttgtataaccatcgtttgggcaatcttggagggtagTTGGAGACGGAACGGGACATGGGAACAAATAAAGGAATATCTGAAAAGCAGATTCGTTTGAAGATTTTTTCTCCAGATGTGTTGAACATTACGTTGGTTG
upper sequence: GLYMA07G30150.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S49_216V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------gtgaatttcaatcgaatttgaatttgaactttactc---aagtgccatatca----ctgtttttgttgatgtagGCTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAGCAGATTCGTTTGAAGATTTTTTCGCCCAATGTTCTCGACATTACGCTTGTGG
|| || |||| || | | ||| | || | || || | | || | | || | | || ||||||| ||||| ||||| |||| |||||| || | ||||| ||||||||||| |||| |||||||| || |||||| | |||||||||||||||
gttgcttcttttgcacgaattattcgttgtcaaagacaattgagtatcg--ttggagttcattcttggcgtactaaatgaggtgccacttctcgggttgcagGCTGAAACTGACAGGGAGCTTGGAACGAACAAGGGGATTTCTGAAAAGCAGATTCGACTGAAAATTTTTTCACCTAATGTTTTGAACATTACGCTTGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgaatttgaatttgaactttactcaagtgccatatcactgtttttgttgatgtagGCTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAGCAGATTCGTTTGAAGATTTTTTCGCCCAATGTTCTCGACATTACGCTTGTGG
tgttgat putative branch site (score: 4)
tttttgtt CT-rich tract
ttgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatttcaatcgaatttgaatttgaactttactcaagtgccatatcactgtttttgttgatgtagGCTGAGACTGATAGGGAAGCTGGAGGGAACAAAGGTGTGTCTGATAAGCAGATTCGTTTGAAGATTTTTTCGCCCAATGTTCTCGACATTACGCTTGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA