Sequence
atgc intronic sequence ATGC exonic sequencegtatttatttgtattttattgcttacactttttttggtcaacaatatctcattctggaccctgtttgcatattttagATGGCAAATGCTGTGCCTGTGCTTTGTGTTGCAAGAAATGTTGCTTGCAATGTTCGTGGTGGTTTCTTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g63820.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g63820.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G019274_T01 (Zea mays), 3'ss of exon 7
------------------------gtatttatttgtattttattgcttacactttttttggtcaacaatatctcattctggaccctgtttgcatattttagATGGCAAATGCTGTGCCTGTGCTTTGTGTTGCAAGAAATGTTGCTTGCAATGTTCGTGGTGGTTTCTTCAG----
| || | | | | || ||| || |||| | | || || || | | | | | |||||||||||| |||| ||| |||| || ||||||||||| |||||||||||||||||||||||||| | |||||
ttatttatgaagatatttgtatgcatgttcactgttctgtttcggctgacgtgttttcta-tacccattaaagaatgatatgtgttttctataaattttagATGGCCAATGTTGTTCCTGGTCTATGTGTTGCAAGGAATGTTGCTTGCAATGTTCGTGGTGGGGTTTTCAGGTTG
upper sequence: LOC_Os01g63820.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G019274_T01 (Zea mays), 3'ss of exon 4
------------------------gtatttatttgtattttattgcttacactttttttggtcaacaatatctcattctggaccctgtttgcatattttagATGGCAAATGCTGTGCCTGTGCTTTGTGTTGCAAGAAATGTTGCTTGCAATGTTCGTGGTGGTTTCTTCAG----
| || | | | | || ||| ||| |||| | | || || || | | | | | |||||||||||| |||| ||| ||| || ||||||||||| |||||||||||||||||||||||||| | |||||
ttatttatgaagatatttttatgcatgttcactgttctgtttcggctgacatgttttcta-tacccattaaagaatgatatgtgttttctataaattttagATGGCCAATGTTGTTCCTAGTCTATGTGTTGCAAGGAATGTTGCTTGCAATGTTCGTGGTGGGGTTTTCAGGTTG
upper sequence: LOC_Os01g63820.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G039650_T02 (Zea mays), 3'ss of exon 4
gtatttatttgtattttattgcttacactttttttggtcaacaatatctcattctggaccc-------tgtttgcatattttagATGGCAAATGCTGTGCCTGTGCTTTGTGTTGCAAGAAATGTTGCTTGCAATGTTCGTGGTGGTTTCTTCAG
||| ||||| |||||||| || |||| || | |||| | |||| |||| | | | | |||||||||||| |||||||| || || || ||||||||||| |||||||||||||||||||||||||| || |||||
gtacttatt---attttattactc-tgtattttgtgttgaacatatacccattatggaatgatatgtatttctataaattttagATGGCCAATGCTGTTCCAGTTCTATGTGTTGCAAGGAATGTTGCTTGCAATGTTCGTGGTGGGTTTTTCAG
upper sequence: LOC_Os01g63820.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G42790.1 (Glycine max), 3'ss of exon 4
-gtatttatttgtattttattgc---ttacactttttttggtcaacaatatctcatt------ctggaccctgtttgcatattttagATGGCAAATGCTGTGCCTGTGCTTTGTGTTGCAAGAAATGTTGCTTGCAATGTTCGTGGTGGTTTCTTCAG-
|| | | ||||| ||| ||| || | ||||||| || || | || || | || | | ||||| ||| |||||||| || || || ||||| |||||||||||||| |||||||| | ||| |||| ||||
tgtgggtttatgtatattactgcattttttaatttttttttctaaatattcatgatagagacactaatatattcttttctttattagaCGGCCAATGCTGTCCCAGTCCTATGTGTAGCAAGAAATGTTGCATGCAATGTCAGAGGTTGTTTTTTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacactttttttggtcaacaatatctcattctggaccctgtttgcatattttagATGGCAAATGCTGTGCCTGTGCTTTGTGTTGCAAGAAATGTTGCTTGCAATGTTCGTGGTGGTTTCTTCAG
tgcttac putative branch site (score: 2)
atatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttatttgtattttattgcttacactttttttggtcaacaatatctcattctggaccctgtttgcatattttagATGGCAAATGCTGTGCCTGTGCTTTGTGTTGCAAGAAATGTTGCTTGCAATGTTCGTGGTGGTTTCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG