Sequence
atgc intronic sequence ATGC exonic sequence...cttctttaattctaccactctactcaggtgcacttgatctaattgtctgttcttttctgtttcatgaagctcttgatttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 7
cttctttaattctaccactctactcaggtgcacttgatctaattgtctgttcttttc---tgtttcatgaagctcttg--atttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG
| || | | || || | | || || || || | || | ||| | ||||| ||| ||| | | | ||||| |||||||||||| ||||||||||||||||||||||||||||| || || | || ||||||||| | |||| | |||||||| ||||| |
--taactactcttgatgctttaat---acctgatgaattaaactgctcagtcatgtcaggcaatacattgtgttcttgtcattcaaatctattctctctattcagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCATTCAAACTCCACATTCCAAGAGTCCACGATTACCTATGGATTGCAGAAGATG
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g04690.1 (Oryza sativa), 3'ss of exon 9
------cttctttaattctaccactctactcaggtgcacttgatctaattgtctgttcttttctgtttcatgaagctcttgatt-tcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG
||| | | ||||| | | || | | |||||| || | | | | | ||||| | || | | | | | ||||| ||||||||||||| |||||||| ||| |||| ||||||||||| || | || ||||||||||| || | |||| |||||| | |||||||| |
gtaaattgaagacaatgacaactctctaaaaaaaagagctcttcttgttcttctgtttactttgatgccttta--ttactgattgttgtgattttttttaaatgcagGTATTAAATATGCTTTCTTGCTGGATAGAAAATCCTAACTCAGAGGCATTCAGATTTCATATTCCAAGGGTTCATGATTACTTGTGGGTCGCTGAAGATG
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os11g08569.1 (Oryza sativa), 3'ss of exon 7
-cttctttaatt--ctaccactctactcaggt-gcacttgatctaattgtctgttcttttctgtttcatgaagctcttgatttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG
|| |||| | | ||| | ||| || ||| | || | | | || | |||| || | || | || ||||| |||||||| ||| ||||||||||||||||||| ||||||||| || || | |||||| || | | | | ||||||| ||||| ||||||||||
ctgtcagaaattagtttatgccctagtgtggttacatttgtttc--ccatcagcttgtcactaatagctgaaaaataaaataactaagtaaattat--acacagGCATTAAATATCCTTGCTTGCTGGATTGAAGATCCAAGCTCAGAGGCATTCAAATGCCATATTGCACGCGTATATGATTATTTATGGATCGCTGAAGACG
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 7
cttctttaattctaccactctactcaggtgcacttgatctaattgtctgttcttttctgtttcatgaagctc--ttgatttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG
| || | || | | | | | || || || | | || || | || || | || ||||| || | | | ||||||||| |||||||||||| |||||||||||||||||||||||||||||||| || | || || ||| || | | | | || |||||| |||||||||| |
-atgttcagttattgctcatatgttgcgaaacttttatatatagatttcttgattatttcttaatattgttcaactgattgcc-gcaagaaattctgtacagGTATTAAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGCCTTCAAACTCCACATCCCACGAGTCTATGACTACTTGTGGCTTGCTGAAGATG
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G341010_T01 (Zea mays), 3'ss of exon 7
-cttctttaattctaccactctactcaggtgcacttgatctaattgtctgttcttttctgtttcatgaa--gctcttgatttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG
| | | | ||| | | || | | ||| | | | |||| || || |||| | | | || | | | |||||| || ||||||||| || ||||||||||| |||||||||||||| || ||| | ||| |||| |||||| | ||||||||||| |||||||||| |
aagtgtgtgccttagtgactagatt--agtataatattcttaactattcctataagcttgttccacaaattgctcccaaatatcaaataa-tattatacacagGTATTGAATATGCTTGCTTGTTGGATTGAAGACCCAAACTCAGAGGCATTCAAGCTCCATGTTCCTCGAATTTATGATTATTTGTGGCTTGCTGAAGATG
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G469298_T01 (Zea mays), 3'ss of exon 3
cttctttaattctaccactctactcaggtgcacttgatctaattgtctgttcttttctgtttcatgaa--gctcttgatttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG
| | | | ||| | | || || || | | | | |||| |||||| |||| | | || | | | |||||| | ||||||||| |||||||||||||||||||||||||||| || || | ||| | || |||||| | |||||||||||||||||||||| |
-gtgtgtgccttagtgactagattagtatgatatttctcaactatttcctataagcttgttacatgaatcgctcccaaatattaaataaa-gttatacacagGTACTGAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCAGAGGGATTCAAACTCCATGTACCTCGAATTTATGATTATTTGTGGATTGCTGAAGATG
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 5
cttctttaattctaccactctactcaggtgcacttgatctaattgtctgttcttttctgtttcatgaagct-cttgatttcctgttatctga---tttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG
|| | | | | | | | ||| | ||| ||| | | || | |||| | | | | | || | |||| || | ||| ||||| || ||||||||| ||||||||||||||||||||||| |||||||| || | ||||| ||| || | | | |||| |||||| |||||||||| |
----ccagtttatgctcatagattgtgaaacttttgttataagtgtacagtatattttatttcttaacgttgttcgactgattgttgcaagaaattctgtgcagGTATTGAATATGCTTGCTTGCTGGATTGAAGATCCAAACTCGGAGGCCTTCAAACTTCATATCCCACGAGTCTATGATTACTTGTGGCTTGCTGAAGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgttcttttctgtttcatgaagctcttgatttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG
atctgat putative branch site (score: 4)
ttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttctttaattctaccactctactcaggtgcacttgatctaattgtctgttcttttctgtttcatgaagctcttgatttcctgttatctgatttgtacagGTGTTAAATATGCTTTGCTGCTGGATTGAAGATCCAAACTCAGAGGCCTTTAAGTTGCATATTCCAAGAATTTTTTATTATTTGTGGATTGCTGAAGACG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - -ctaccac
- - - - - - - - - - - - - - -gcacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcctgt