Sequence
atgc intronic sequence ATGC exonic sequence...ttcaaattgcacaataatcttttttaagacaagattttgccccactcatcgtttttgttggataattatctctactgatgctcttcttttgttggtgcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
Basic information
species | Oryza sativa |
transcript | LOC_Os08g25734.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 1
------ttcaaattgcacaataatcttttttaagacaagattttgccccactcatcgtttttgttgga--taattatctctactgatgctcttcttttgttggtgcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
|| | || || | || || | || || | ||| ||| | | | | | | | | | | | | |||||||| |||||||| |||||||||||||| ||||||||||| |||||||||||||| ||| | || |||||||||||||||||||| ||||| ||||||||||||| |
ataatttttcagtttcagagctgtccttgtcc--------ttctgtggtgcccattagtttactcactcttggctgtatacaataacacacatttgttgttggttcagAGTGTTCTTGGAATCATTCTGGGAGGTGGTGCTGGGACTAGATTGTACCCCTTGACAAAGAAGCGTGCCAAGCCTGCAGTGCCATTGGGTGCCAACTATA
upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G163437_T03 (Zea mays), 3'ss of exon 1
ttcaaattgcacaataatcttttttaagacaagattttgccccactcatcgtttttgttggataattatctctactgatgctcttcttttg-ttggtgcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
||| | | | | || | | | | | | ||| ||||| |||||||| |||||||||||||| ||||||||||| |||||||||||||| ||| | || |||||||||||||||||||| ||||| ||||||||||||| |
--------------------------------------------------gttcactcttggctgtataccataataacacacatttgttggttggttcagAGTGTTCTTGGAATCATTCTCGGAGGTGGTGCTGGGACTAGATTGTACCCCTTGACAAAGAAGCGTGCCAAGCCTGCAGTGCCATTGGGTGCCAACTATA
upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G163437_T01 (Zea mays), 3'ss of exon 1
ttcaaattgcacaataatcttt---tttaagacaagattttgccccactc--atcgtttttgttggataattatctctactgatgctcttcttttg-ttggtgcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
| ||| |||| ||| ||| ||| | || || || || | | |||| | || | || | | | | | | ||| ||||| |||||||| |||||||||||||| ||||||||||| |||||||||||||| ||| | || |||||||||||||||||||| ||||| ||||||||||||| |
----gagtgc-taatagattttgaatttcagagctgtcagtgtccatttctgatgttcactcttggctgtatacca-taataacacacatttgttggttggttcagAGTGTTCTTGGAATCATTCTCGGAGGTGGTGCTGGGACTAGATTGTACCCCTTGACAAAGAAGCGTGCCAAGCCTGCAGTGCCATTGGGTGCCAACTATA
upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 1
ttcaaattgcacaataatcttttttaagacaagattttgccccactcatcgttt--ttgttggataattat--ctctactgatgctcttcttttgttggtgc----agAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
| | | |||||| ||| | | | | ||||| | ||| | ||| | ||| | || | |||| || ||||||||||||| || || |||||||||||||| |||||| | | ||||| || ||||||||| | || ||||| || || ||||| || || ||||| |
--------atgaatttttttttttttagatcacaatagtgaattttgatcgtgcgatatttgattgattctggttctgattgtgattgcaatttgaaaatgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGTCTTTATCCACTGACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA
upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 1
--ttcaaattgcacaataatcttttttaagacaagattttgccccactcatcgtttttgttggataattat--ctcta---ctgatgctcttcttttgttggtgcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
|| | || ||||||| | || | ||| ||| | | | | ||| | | || | ||| ||||| | | | | | ||||||||||||| || || |||||||||||||| |||||| | | ||||| |||||||||||| | || ||||| || || ||||| || || ||||| |
tttttagat--cacaatagt-----ttgaattttgatcttgtgatatttgtattggatgtggattggttctggttctgattctgattccaatttaaaatgtttatagAGTGTGCTTGGCATTATACTTGGAGGTGGTGCTGGGACTCGGCTTTATCCACTCACCAAGAAGAGGGCAAAGCCAGCTGTTCCTCTTGGAGCTAACTATA
upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDP04344 (Chlamydomonas reinhardtii), 3'ss of exon 3
ttcaaattgcacaataatcttttttaagacaagattttgccccactcatcgtttttgttggataattatctctactgatgctcttcttttgttggtgcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
| | | | |||| | || || | | | | | | || | ||| | |||||| ||||| || || ||||| || |||||||| || || | ||||||| || |||||||||||||||||||| || ||||| ||||| ||||||||
------------------------gtatgctcgcgctggcccatttgatgcttccggactcgtcgatgtgaccg-tcccgccatctcgttgccgatgcagACGGTGCTGGGTATTATTCTGGGTGGTGGTGCCGGCACCCGTCTGTATCCTCTGACCAAGAAGCGTGCCAAGCCGGCGGTGCCCCTGGGCGCCAACTATC
upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S2_337V6.1 (Physcomitrella patens), 3'ss of exon 1
--ttcaaattgcacaataatcttttttaagacaagattttgccccactcatcgtttttgttggataattatctctactgatgctcttcttttgttggtgcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
| || || || | ||| ||| | | || || || || ||| || | | | || | | | || |||||||||||||||| || ||||| || || || |||||||| | |||||||| | ||||| |||||||||||||| || ||||| | |||||||| |||
agtgagaaatgtttgctact-tttcttacgtctgaatagtgttt-gtgtgtctttaagtttgcattaccttagcctgatttgatatgtatccatttctgcagAGTGTGCTTGGTATAATTCTAGGTGGCGGAGCAGGGACACGTTTGTATCCTTTGACCAAAAAGCGTGCCAAGCCAGCTGTGCCGATAGGTGCCAATTACC
upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S76_105V6.1 (Physcomitrella patens), 3'ss of exon 1
ttcaaattgcacaataatcttttttaaga---caagattttgccccactcatcgt-ttttgttggataattatctctactgatgctcttcttttgttggt---gcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
|||| || | ||| ||| | | ||| ||| | |||| || |||| | || | | | | | ||||||| ||||||||| || |||||||||||||| ||||| ||||| | | || | ||||| | || ||||||||||| ||||| |||||||| ||||| |||||||||
-------tgcatgatcttgagatttgagaatcttgtgtcgagatccaatcagaatgttttattaattaatgagctttggcaaacattcttctatgttggttttgcagAGTGTACTAGGAATCATTCTTGGTGGTGGAGCAGGAAGTCGACTTTATCCATTAACTAAGAAGCGTGCGAAGCCAGCCGTGCCACTGGGCGCCAACTACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatcgtttttgttggataattatctctactgatgctcttcttttgttggtgcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
tactgat putative branch site (score: 2)
tgctcttcttttgtt CT-rich tract
ataattatct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaaattgcacaataatcttttttaagacaagattttgccccactcatcgtttttgttggataattatctctactgatgctcttcttttgttggtgcagAGTGTGCTTGGAATCATTCTTGGAGGTGGTGCAGGGACTAGATTGTATCCCCTCACCAAGAAGCGTGCCAAGCCTGCCGTGCCTCTGGGTGCCAACTACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC