Sequence
atgc intronic sequence ATGC exonic sequence...cctttcatcattattcataaaaaatcaaattccccatgctcgatcacaatgttttcatgacatttcatctaatatatgagtcctgtctctcacaatgcagAAAGTCTTTGACCATGACACGTTCTCTGCTGATGACATAATGGGAGAAGCCGAGATTGACATCCAACCCCTGATAACATCCGCCATGGCATTTGGAAATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os02g49070.1 (Oryza sativa), 3'ss of exon 8
cctttcatcattattcataaaaaatcaaattccccatgctcgatca--caatgttttca--tgacatttcatctaat----atatgagtcctgtctctcacaatgcagAAAGTCTTTGACCATGACACGTTCTCTGCTGATGACATAATGGGAGAAGCCGAGATTGACATCCAACCCCTGATAACATCCGCCATGGCATTTGGAAATG
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------ggaagcatttatggaa--tgaagtacccttatataaagcagccaatatgaaaagctgtcttttcactgaatccaaataacataataatctctctattttcagGAAGTATACGACCATGATACGTTCTCTGCTGATGATATCATGGGGGAAGCGGAGATAGATCTTCAACCAATGATCACAGCCGTCATGGCCTTTGGAGATC
upper sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA09G02830.1 (Glycine max), 3'ss of exon 8
---------------cctttcatcattattcataaaaaatcaaattccccatgctcgatcacaatgttttcatgacatttcatctaatatatgagtcctgtctctcacaatgcagAAAGTCTTTGACCATGACACGTTCTCTGCTGATGACATAATGGGAGAAGCCGAGATTGACATCCAACCCCTGATAACATCCGCCATGGCATTTGGAAATG
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aatgcatctcgctgtgtgtgtgtgtttgtacatgggaaagaagataactgattgttggtttgagaat----atgacacttcatgttatcaat------tgtctgt-----tgcagAAAGTATTTGACCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCAGACATTGATCTTCAGTCTCTGATAACATCTGCTATGGCATTTGGAGATG
upper sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G13700.1 (Glycine max), 3'ss of exon 8
-------------cctttcatcattattcataaaaaatcaaattccccatgctcgatcacaatgttttcatgacatttcatctaatatatgagtcctgtctctcacaatgcagAAAGTCTTTGACCATGACACGTTCTCTGCTGATGACATAATGGGAGAAGCCGAGATTGACATCCAACCCCTGATAACATCCGCCATGGCATTTGGAAATG
| | | | | ||| ||| | || | || | | | | | |||||| ||||||| || || ||||| | |||||||||| ||||| |||||||| || ||||||||||| |||||||||||||| || ||||| | || | ||||||||||| || |||||||||||| |||
ttccctattctctctgtgtgtgtctgtacatgggaaagaagataactgatttttggtttgagaat----atgacacttcatcttatcaat------tgtctgt---gctgcagAAAGTATTTGATCATGACACATTTTCTGCTGATGATATAATGGGAGAAGCAGACATTGATCTTCAGTCTCTGATAACATCTGCTATGGCATTTGGAGATG
upper sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G13070.1 (Glycine max), 3'ss of exon 6
---------------------------------------------------------------------------------------------cctttcatcattattcataaaaaatcaaattccccatgctcgatcacaatgttt----tcatgacatttcatctaatatatgagtcctgtctc--tcacaatgcagAAAGTCTTTGACCATGACACGTTCTCTGCTGATGACATAATGGGAGAAGCCGAGATTGACATCCAACCCCTGATAACATCCGCCATGGCATTTGGAAATG
||| || | | || | | | | | | || | | | | |||| | || | || | | | ||| | | || ||||||| || ||||| ||||| ||| || ||||||||||||||||| ||||| || ||||| | || ||||||||||||||||| || |||| || |||
gtaagattgaatttcatcttgtattgttagaaaatggaaacaaattctgtgatgcttattcggtgtttggatatttggatcttcatgtgtgatacttctatttgtctgtatgtgtgttttggtacagaagatacaaaattgatttctggtgtaaaaacatgtaattttatcc-taactgctggttacattgcattgcagAATGTATTTGATTATGACTTGTTTTCGGCTGATGACATAATGGGGGAAGCAGATATTGATCTTCAGCCCCTGATAACATCCGCAATCGCATACGGTGATG
upper sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT4G21160.4 (Arabidopsis thaliana), 3'ss of exon 7
------cctttcatcattattcataaaaaatcaaattccccatgctcgatcacaatgttttcatgacatttcatctaatatatgagtcctgtctctcacaatgcagAAAGTCTTTGACCATGACACGTTCTCTGCTGATGACATAATGGGAGAAGCCGAGATTGACATCCAACCCCTGATAACATCCGCCATGGCATTTGGAAATG
||| | |||| |||| ||| | | | || ||| | || || || | ||| || | || | | ||| | | |||| |||| |||||| ||||||| || |||||||||||||||||||||||||| |||||||| ||||| || ||||| ||||| || ||||| |||||| |
gtaaaagcttggtctaatatttccaaaa--tca--ctttctactcttgatga--atcattacagaagtttttcccttacatttta----tgttttt------gcagCAAGTGTTTGACTATGACACATTTTCTGCTGATGACATAATGGGAGAAGCTGAGATTGATATCCAGCCTCTGATTACATCTGCAATGGCTTTTGGAGACC
upper sequence: Vv10s0003g04900.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT4G05330.1 (Arabidopsis thaliana), 3'ss of exon 8
cctttcatcattattcataaaaaatcaaattccccatgctcgatcacaatgttttcatgacatttcatctaatatatgagtcctgtctctcacaatgcagAAAGTCTTTGACCATGACACGTTCTCTGCTGATGACATAATGGGAGAAGCCGAGATTGACATCCAACCCCTGATAACATCCGCCATGGCATTTGGAAATG
| | | |||| | || | || |||| || | || | | || || || ||| | | | | | ||||| |||| | ||| |||| || || |||||||||||||||||||||||||| || ||||| || ||||| |||||||||| || ||||| ||||| ||
-------------gtaagagcaaattca-ttttctattgacgatttcagtcattgccaaagcttatatata-tatcttacggtttcttatgtggttgcagCAAGTGTATGATTATGATACATTTTCTGCTGATGACATAATGGGAGAAGCAGATATTGATATACAACCTTTGATAACATCTGCAATGGCTTTTGGGGATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaatgttttcatgacatttcatctaatatatgagtcctgtctctcacaatgcagAAAGTCTTTGACCATGACACGTTCTCTGCTGATGACATAATGGGAGAAGCCGAGATTGACATCCAACCCCTGATAACATCCGCCATGGCATTTGGAAATG
ctctcac putative branch site (score: 3)
tcctgtctctc CT-rich tract
atttcatctaatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctttcatcattattcataaaaaatcaaattccccatgctcgatcacaatgttttcatgacatttcatctaatatatgagtcctgtctctcacaatgcagAAAGTCTTTGACCATGACACGTTCTCTGCTGATGACATAATGGGAGAAGCCGAGATTGACATCCAACCCCTGATAACATCCGCCATGGCATTTGGAAATG
cctttca
- - - - - - - - - aaaaaat
- - - - - - - - - - - - - - -ttcccca
- - - - - - - - - - - - - - - - - - - - - - cacaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgac
