Sequence
atgc intronic sequence ATGC exonic sequence...attcttgttggcttatccaaaaaaacaaaactactgttgagcatatgattgcatatatgtacaatgaactaatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g57660.2 (Oryza sativa), 3'ss of exon 6
attcttgttggcttatccaaaaaaacaaaactactgttgagcatatgattgcatatat-gtacaatgaactaatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
|| | | | | | ||| || | ||| | || ||| | | | || ||| ||| || | | | ||||||||||||||||| |||||||| |||||||| ||||| ||||| | || ||| |||||||||||||||||||||| |||||||| |||||| | |||||
------------gtaacggatttatctacacttcttt--agc-tccaatcccatttcttgcgcagtga--caatccttaacacttgc-----aaattgcagTTTCGCTTTGTTGTAATGGGTAACATGTTTTGCACGGAATTGAGGATTCATCGGAGATTTGATTTGAAAGGTTCATCCTTAGGCCGTTCTACTGACAAAA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 5
---attcttgttggcttatccaaaaaaac--aaaactactgttgagcatatgattgcatatatgtacaatgaactaatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
| | ||| | |||| || | | || | | | | | | | | |||| | | || || | | ||| | | | || ||||||||| ||||| ||||||||||||||||| ||||| ||||| ||||||| |||| |||||||||||||| || || ||||| |||||| | || ||
gtaactattgacatcagcaccaatttcacttgaggtttctttagtttaattttcccccttcctttttaatgtaatgatccttcttgaatatctgcaaatt-gcagTTTCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATCCACCGGAGGTTTGATTTGAAAGGATCATCTTTAGGCCGTTCTACTGATAAAA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G076392_T02 (Zea mays), 3'ss of exon 4
--attcttgttggcttatccaaaaaaacaaaactactgttgagcatatgattgcatatatgtacaatgaactaatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
| | | || | | || ||| | | | | ||| | |||| ||| | ||| || | | | | | | | ||| | ||||||||| || |||||||| |||||||||||||| ||||| ||| | |||| || |||| ||||| ||||||||||| |||||||| || || ||||||| |
ctagtgtcattttcatttcttaaacagtcagagca--gtttatgatatcatttaaattatagtcatttatcccaaaataatgcatgttgttcgtgtttgcagTTCCGGTTTGTAGTGATGGGAAACATGTTTTGCACTGAACTTAGAATTCACCGGAGGTTTGACTTGAAAGGTTCATCCTTAGGCCGCTCAACAGACAAAG
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 5
attcttgttggcttatccaaaaaaacaaaactactgttgagcatatgattgcatatatgtacaatgaactaatttttgtaaactatgtcc-tactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
| || ||| | | |||| | | || | || | | | || | || || | || || || | ||||||| || ||||| ||||||||||||||||| ||||| ||||| |||| || |||| |||||||||||||| || || ||||| || ||| | |||||
----gtaatgatttacatgagcat-caaattcatt--------taaggtttctttagtttagtttttaccctccctttttaatgatatctgcaaactgcagTTCCGGTTTGTTGTAATGGGAAACATGTTTTGCACTGAATTGAGAATTCACCGGAGGTTTGATTTGAAAGGCTCGTCTTTAGGCCGCTCTACTGACAAAA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 5
attcttgttggcttatccaaaaaaacaaaactactg----ttgagcatatgattgcatatatgtacaatgaactaatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
| | | |||| | || ||| || | || | | | ||| | || ||||| || || || | ||| |||||||||||||||||| ||||||||||| |||||||||||||||||| | ||||||||||||| ||||||||||||||| || | || |||||| | ||||||
---caaatgtaccacatcaaatatttgaacctatcatgacttaataatctaaattt-tatctcattaagaggctaatacttatatctaattttctattttgcagTTTCGCTTTGTCGTAATGGGAAATATGTTCTGCACAGAATTAAGGATCCATAGGAGATATGATTTGAAAGGTTCATCTCTTGGACGTTCTTCGGACAAGA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 5
attcttgttggcttatccaaaaaaacaaaactactgttgagcata------tgattgcatatatgta--caatgaactaatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
| ||||| || ||| || | ||| | | || || || | || ||||| || || || | ||| |||||||||||||||||| || |||||||| |||||||||||||||||| | ||||||||||||| ||||||||||||||| || | || |||||| | ||||||
--------ccaaaaaaaaaaaaagacttaacatctttcatgcaaaatgacttaataatctacattttatcaggaggctaatacttatatctaattttctattttgcagTTTCGCTTTGTCGTGATGGGAAATATGTTCTGCACAGAATTAAGGATCCATAGGAGATATGATTTGAAAGGTTCATCTCTTGGACGTTCTTCGGACAAGA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 4
attcttgttggcttatccaaaaaaacaaaact---actgttgagcatatgattgcatatatgtacaatgaactaatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
| | | | | | || |||| | | | ||| | | | ||||| ||| | | || | || ||||||||||||||||| ||||||||||| |||||||||||||| ||| | |||||| |||| |||||||| |||||||| ||| | || | || ||||||||
---atgatcaaatatttgagcctatcataacttgcatcttcaatttcatgtacatttcctcaaataggaggctaatacttgaatatgattttctgtcttgcagTTTCGCTTTGTTGTAATGGGAAATATGTTCTGCACAGACTTAAGGATCCATCGGAGGTTTGATTTAAAAGGTTCTTCCCTTGGAAGATCATCAGACAAGA
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------------------------------------------attcttgttggcttatccaaaaaaacaaaactactgttgagcatatgattgcatatatgta-caat----gaactaatt---tttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
| | | | | | | | || ||| || | ||| | || | |||| |||||| | |||| ||| | | || | | |||||||| || ||||| || ||||| |||||||||| ||||| || |||||||| |||||||||| | |||||||| ||||| || || ||||||||||| |
gtcctgaaccaaaatacctcaagattctgattttgattttttattatcattagctttgaagttgccgacattgctgcctctaaatatgatgtagagtagaactctaacattagagcaacatttggaaatccaaatcaatcttaaaactaactatgtttgaaaatt-tctcttccattgcagTTCCGTTTTGTGGTGATGGGTAACATGTTCTTTACAGATCTAAGAATCCATCGGAGATTTGACCTTAAAGGTTCGTCCTTGGGACGCTCTGCAGACAAAG
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ34272 (Selaginella moellendorffii), 3'ss of exon 4
attcttgttggcttatccaaaaaaacaaaactactgttgagcatatgattgcatatatgtacaatgaac-taatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
| ||| | || | | | || ||| || | |||| || ||| ||| |||| |||||||||||||||||||||||||||||||| | || || || |||| || |||||||| || || || | ||||| || | || || |
------------------------------------------gtttgagt---tactcggtccttaaatgcgattacagtctaacatgtgct--tttacagGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACACCGGAGGTTCGATTTGAAGGGGTCGTCACTGGGGCGGTCGACGGAAAATG
upper sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ31327 (Selaginella moellendorffii), 3'ss of exon 4
attcttgttggcttatccaaaaaaacaaaactactgttgagcatatgattgcatatatgtacaatgaac-taatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
| || | | || |||| || | |||| || ||| ||| |||| |||||||||||||||||||||||||||||||| | || || || |||| || |||||||| || || || | ||||| || | || || |
------------------------------------------------------gtttggtccttaaatgcaattacagtctaacatgtgct--tttacagGTTCGTTTTGTAGTAATGGGAAACATGTTCTGCACAGACCTTCGTATACACCGGAGGTTCGATTTGAAGGGGTCGTCGCTGGGGCGGTCGACGGAAAATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattgcatatatgtacaatgaactaatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
aactaat putative branch site (score: 2)
tcctacttt putative PPT
taatttttgtaaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcttgttggcttatccaaaaaaacaaaactactgttgagcatatgattgcatatatgtacaatgaactaatttttgtaaactatgtcctactttgcagTTTCGCTTTGTAGTAATGGGAAACATGTTCTGCACAGAATTACGAATCCATAGGAGATTTGATTTGAAAGGTTCCTCCTTAGGGCGTTCTGCAGACAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - -tgttggc
- - - - - - - - - aaaaaaa
- - - - - - - - - - - - - aaaacta
- - - - - - - - - - - - - - - - -ctgttga
- - - - - - - - - - - - - - - - - - - - gcatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtcc