Sequence
atgc intronic sequence ATGC exonic sequence...gatgatgtatagcatatccaccaagaaccaccatataaattaacctttccaccttgctcaactacaaatggactgactcatctttctttttgaccctcagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g19850.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G10390.1 (Glycine max), 3'ss of exon 4
gatgatgtatagcatatccaccaag--aaccaccatataaattaacctttccaccttgctcaactacaaatggactgactcatctttctttttgaccctcagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
| | || || | | | ||| || | | || ||||| | || | || | | | | | | || | | || | ||||||| || |||||||||||||| ||| | || |||||||| |||||||||||||| ||||| | || || ||||| || ||||| |||||||||||
aaagcagtttattaaaaaaaagaagcaaatcctaacatgcattaagtaggctctattaataaatgata--tagtttagtattttcttgtgtatgttctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
upper sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
gatgatgtatagcatatccaccaagaaccaccatataaattaacctttccaccttgctca-actacaaatggactgactcatctttctttttgaccctcagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
| | | || | | | || ||| | |||| | | | || | | | | | || | | | || | | || | ||||||| || |||||||||||||| ||| | || |||||||| |||||||||||||| ||||| | || || ||||| || ||||| |||||||||||
-tttgtaaaaagaaaagcagttttttccccccaaaaaaatctaattctaacactcattaataattgatatagtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
upper sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 5
----gatgatgtatagcatatccaccaagaaccacca-tataaattaacctttccaccttgctcaactacaaatggactgactcatctttctttttgaccctcagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
|| | | || | || | | | || ||||| || | | ||| ||| | | || | | || || ||||||| || || || ||||||||||| | || |||||||| |||||||||||||| |||||| | ||||||||||||||||||||||| || ||| ||
ctttcataactcttgttttactggcttaggcttccttctttttgttgtcctttttgtattaattga-taccaatctattttcttgacatctttgtt----tctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
upper sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S22_329V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------gatgatgtatagcatatccaccaagaaccaccatataaattaacctttccaccttgc----tcaactacaaatggactg--actcatctttctttttgaccct-cagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
|| || || | | | |||| | | | | | | | || || | || | | | | | | ||| | || || | | |||||||| || || |||||||| || || ||||||||||||| || ||||| || ||||| ||| | ||||||||||| || || || ||||| |||||||
gttggtttttgttttctaaaagcatttgcataccatcgtgtttgattgagactttgtctttaaatccacatgtttgatctagtagtacgtagtgcagttgaggtcaatgagattgtaccaacttcttgactgctttctggacatttcgatttcgagtgaaggtacatagcaactaggttaactgttgtgcaatgcagGGTGGGGGTCCATACTATCTGATAGGACGGGCACTTGGTCCTGAGGTTGGCGTGAGTATCGGACTCTGTTTCTTCCTGGGAAACGCTGTTGCTGGAGCTA
upper sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S139_48V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------------------------------gatgatgtatagcatatc-caccaagaaccaccatataaattaacctttccaccttgctcaa--ctacaaatggactgactcatctttctttttgaccctcagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
||| || | |||| ||| | || | | || || | | | | | |||| | | || | | || || ||||||||| || |||||||| || || || ||||||||||||| || ||||| || |||||||| | |||||||||||||| || || || || | || |
gtttgttgtcgtttcctaagcatttacgaattaacacgcttgattgagactgtattttatagtggaagtggttgatctaataatacacaatgcatttgaggtcaataatattgcacttactgcctggccacttgctcacattgctatttggaaggaagttacatcagaatggaattaatgtttccttaa---ttcagGGTGGGGGTCCTTACTACCTGATAGGACGGGCACTTGGTCCTGAGGTTGGTGTGAGTATTGGTCTCTGTTTCTTCCTTGGAAACGCTGTGGCTGCCGCAA
upper sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S5_444V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------gatgatgtatagcatatccac-caagaaccaccatataaattaacctttccaccttgctcaactacaaatggactgactcatctttctttttgaccctcagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
| | | || | || | || || | | || | ||| | | | | || | | || | | | || || | |||||||| || || || || || || || |||| |||||||| || |||||||| ||||||||||||||||||||||| || ||||||||||| | | |
gttagtatcttgagtaaaggaatttcatgtgtcgaaattcaatcaatcatgtatttgcaatactcttgtctcaaggacatatgcatgtaaatcatttaaggactttatatttgaagca-gtttgtcttccataagattccaacgttttatcattctatta-cagGGTGGGGGTCCCTATTACCTGATAGGTCGGGCTCTTGGTCCAGAGGTTGGAGTAAGTATTGGATTGTGTTTCTTCCTGGGCAATGCAGTTGCTGCATCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttccaccttgctcaactacaaatggactgactcatctttctttttgaccctcagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
ctcatctttctttttg CT-rich tract
tttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatgatgtatagcatatccaccaagaaccaccatataaattaacctttccaccttgctcaactacaaatggactgactcatctttctttttgaccctcagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
-atgatgt
- - - - - - - - - -accaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctacaaa