Sequence
atgc intronic sequence ATGC exonic sequence...gaagcttaagtcagcttggtcatctattgtttttgccttcctagaatctaatcatgttattttggcttttaacattttaaattacttgtggacctttcagGATGCAGATGCTTCTATTCGCAAGAGGGCCCTTGAACTTGTTTTTTTGTTAGTCAACGATACAAATGTAAAGCCTTTGACTAAAGAGCTTGTCGACTACT
Basic information
| species | Oryza sativa |
| transcript | LOC_Os02g56110.2 |
| intron # | 7 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g56110.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G054210_T01 (Zea mays), 3'ss of exon 7
gaagcttaagtcagcttggtcatctattgtttttgcct--tcctagaatctaatcatgttattttggcttttaacattttaaattacttgtggacctttcagGATGCAGATGCTTCTATTCGCAAGAGGGCCCTTGAACTTGTTTTTTTGTTAGTCAACGATACAAATGTAAAGCCTTTGACTAAAGAGCTTGTCGACTACT
|||| | | ||||| | || ||||| || | | || | || ||||||| ||| ||||| |||| |||| || ||| |||||||||||||| ||||| || |||||||| ||||| ||||||||||||| |||||||||||| |||||||||||||||||||||||||||||||| |||| ||||
-tgtcttaccccccgtaggtcaagtttttttttttactgtttcaagcagtctattttgttattctggtttttattatttctaattgct-gtgtacctttcagGATGCCGATGCCTCCATTCGCAAAAGGGCTCTTGAACTTGTTTATTTGTTAGTCAATGATACAAATGTAAAGCCTTTGACTAAAGAGCTCATCGATTACT
upper sequence: LOC_Os02g56110.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA02G03800.1 (Glycine max), 3'ss of exon 6
gaagcttaagtcagcttggtcatctattgtttttgccttcctagaatctaatcatgttattttggcttttaacattttaaattacttgtggacctttcagGATGCAGATGCTTCTATTCGCAAGAGGGCCCTTGAACTTGTTTTTTTGTTAGTCAACGATACAAATGTAAAGCCTTTGACTAAAGAGCTTGTCGACTACT
| | || ||| || | || | | | | | |||| | | | | | || | | || |||||||| |||||||||| ||||| || || |||||||||||||||| | | || || || || || ||||| ||||| ||| | ||||||||| | || ||
-------gtatttgatttgtcttccctcatt----cagtgacaaagatgagctctgttttacaatccaaggggttgatcatttgactcttaac--ttcagGATTCAGATGCTTCGATTCGGAAAAGAGCCCTTGAACTTGTTTATGTTTTGGTGAATGAGACTAATGTGAAGCCCTTGGCAAAAGAGCTTATAGATTATC
upper sequence: LOC_Os02g56110.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv01s0026g00310.t01 (Vitis vinifera), 3'ss of exon 7
----gaagcttaagtcagcttggtcatct-attgtttttgccttcctagaatctaatcatgttattttggcttttaacattttaaattacttgtggacctttcagGATGCAGATGCTTCTATTCGCAAGAGGGCCCTTGAACTTGTTTTTTTGTTAGTCAACGATACAAATGTAAAGCCTTTGACTAAAGAGCTTGTCGACTACT
| || || | || | || ||| ||||| | || | | | | | | | ||| | | | | | ||| | | |||||||||| |||||||||| ||||| || ||||||||||||||| ||| | | |||| || || | ||||| ||||||||| | |||||||| | || ||
tcgtgtagttt--tttagttgtgttatcggattgtgtcaaaattgccacagcc-acttctaatatacatatagaaagcttgtaactttaatattc--tctttcagGATTCAGATGCTTCAATTCGGAAAAGGGCCCTTGAACTTATTTATGTTCTAGTGAATGACAGCAATGTGAAGCCTTTGGCAAAAGAGCTAATTGATTATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctaatcatgttattttggcttttaacattttaaattacttgtggacctttcagGATGCAGATGCTTCTATTCGCAAGAGGGCCCTTGAACTTGTTTTTTTGTTAGTCAACGATACAAATGTAAAGCCTTTGACTAAAGAGCTTGTCGACTACT
ttttaac putative branch site (score: 2)
cctttc putative PPT
ttattttggcttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaagcttaagtcagcttggtcatctattgtttttgccttcctagaatctaatcatgttattttggcttttaacattttaaattacttgtggacctttcagGATGCAGATGCTTCTATTCGCAAGAGGGCCCTTGAACTTGTTTTTTTGTTAGTCAACGATACAAATGTAAAGCCTTTGACTAAAGAGCTTGTCGACTACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
