Sequence
atgc intronic sequence ATGC exonic sequence...gtcaaagtgtgtgtatatatgtctcttctccatcctttctttagatttcaaaggtaaaaattaggttataatgctagaatgacctgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g36860.1 (Oryza sativa), 3'ss of exon 5
-gtcaaagtgtgtgtatatatgtctcttctccatcctttctttagatttcaaaggtaaaaattaggttataatgctagaatgac--ctgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTC
| |||| | ||| | | | | | | | || | | | | ||| || |||| | | |||| ||| | || |||||||| || ||||| ||||||||||| ||||| | || |||||||| ||| ||||||| |||||||| ||||| ||||||||||| || || || || ||
cttacaagttttggtaattgcacatttacatttgtacctatgtgcatcacgt-gttgacgtttacattttaat--tgaattgacttctgtttcattggcacagGGTTGTGATCAATTATGATTTCCCCACTGGCATTGAAGATTATGTTCACCGGATTGGCAGGACTGGAAGGGCTGGTGCCACTGGTGTGGCCTATACGTTT
upper sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G077125_T01 (Zea mays), 3'ss of exon 5
gtcaaagtgtgtgtatatatgtctcttctccatcctttctt-tagatttcaaaggtaaaaatt-aggttataatgctaga--atgacctgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTC
| | | || | | | || ||| | ||| | | ||| | |||| | | | ||| | || || | || | | || |||||||| || ||||||||||| ||||| ||||| || || || ||||| ||||||||||| ||||| || ||||| ||||||||||| ||||| || |||||
----gaatctcagtccagtttgtttcacttcatatgtgcttgcgggtcctttcggtcagaattcacataaaaataatggagcatttcatgttttctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTATGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT
upper sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G078826_T01 (Zea mays), 3'ss of exon 5
gtcaaagtgtgtgtatatatgtctcttctccatcctttctttaga--tttcaaaggtaaaaattaggttataatgctagaatgacc--tgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTC
| ||| || | | | | || || | |||| | | ||| | | || || | | | | | | | | || | | || |||||||| || ||||||||||| ||||| ||||| || || || || || ||||||||||| ||||| || ||||| ||||||||||| ||||| || |||||
--cttagtcca-gtttgttt-cattttatctgtgcttttgtgggtcctttttttgtcagaatttgcatcaacacggtgaagcgccttttgttttctttacacagGGTAGTGATCAACTATGACTTCCCCACTGGTGTTGAAGACTACGTTCACAGGATTGGCAGGACAGGAAGGGCTGGTGCCACTGGTGTTGCATATACATTT
upper sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA05G08750.1 (Glycine max), 3'ss of exon 11
-----------------------------------gtcaaagtgtgtgtatatatgtctcttctccatcctttctttagatttcaaaggtaaaaattaggttataatgctagaatgacctgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTC
| | ||| | | || || ||| || | | | || | |||| | | | || | ||||||| | | || | |||||||||| |||| ||||| ||||| || ||||| || |||||||| || ||||||||||||||||| || || || |||||||| | |||||||| |||
gttgttaattgtttgttttattgtattttttttattctgaggcccatgtgt-tgggtactttaccca--ctgtagtagaacttgtcttggaaaagtgactattgtatttgacaatgaccataaatatt-ttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
upper sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G00260.1 (Glycine max), 3'ss of exon 7
-------------------gtcaaagtgtgtgtat------atatgtctc---ttctccatcctttct--ttagatttcaaaggtaaaaattaggttataatgctagaatgacctgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTC
||| | | | ||| | || | | || | || | | | | ||| | |||| | | | || || ||||||| | | || | |||||||||| |||| ||||| ||||| || ||||| || |||||||| || ||||||||||||||||| || || || |||||||| | |||||||| |||
gttgttaattgtttgttttatcatgttttttttattctgagacccgtgttgggtactttacccactgtagtgaaattagtcttggaaaagtaaccattgtattttacaatgaccataaatatt-ttgcagGGTGGTTGTCAATTATGACTTCCCTACAGGAGTGGAAGATTATGTTCATAGGATTGGAAGGACTGGAAGAGCTGGAGCCACTGGGCTAGCTTACACTTTC
upper sequence: Vv14s0066g01020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G14610.2 (Arabidopsis thaliana), 3'ss of exon 7
gtcaaagtgtgtgtatatatgtctcttctccatcctttctttagatttcaaaggtaaaaattaggttataatgctagaatgacctgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTC
|| | ||||| || | | || | ||| | || | | || ||| || | ||||| || | | |||||||||||| ||||||||||||| |||| |||||||||||||||||| || || |||||||| ||||| || || || || || || | |||||||| |||
----------gtatgaatatgattc----cagtttcaaattcaaccatcagaattataga--agcatatgatcc--gaatgtagaaatttgat-tcacagGGTGGTGGTCAACTATGATTTTCCAAATGGAGTAGAGGATTATGTCCATAGAATTGGAAGAACTGGAAGAGCTGGAGCAACCGGTCTAGCTTACACCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcaaaggtaaaaattaggttataatgctagaatgacctgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTC
acctgat putative branch site (score: 4)
tcttttatc CT-rich tract
taaaaattaggttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcaaagtgtgtgtatatatgtctcttctccatcctttctttagatttcaaaggtaaaaattaggttataatgctagaatgacctgatcttttatcacagGGTGGTTATCAACTATGATTTCCCAACTGGAGTAGAGGATTATGTGCACAGGATTGGAAGGACTGGTAGGGCAGGTGCCACTGGAGTTGCTTACACATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - gtgtgtg
- - - - - - - - - - -tctcttc
- - - - - - - - - - - - - - -ccatcct
- - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgatc