Sequence
atgc intronic sequence ATGC exonic sequence...acaagttaccaataaattaggcagcttttcaggttgattttatcttactgcaagcaggattttatttgttggtgataaactttcaaatttttatctatagGACGAATGTGGTGTCATTGCCGAATGGTGTATTTGCCCATGTCGTACATATATGGGAAGAGGTTTGTTGGTCCAATTACACCTACAATTATTTCTTTGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 5
------------------------acaagtta-ccaataaattaggcagcttttcaggttgatt--ttatcttactgcaagcaggatt--------ttatttgttggtgataaactttcaaatttttatctatagGACGAATGTGGTGTCATTGCCGAATGGTGTATTTGCCCATGTCGTACATATATGGGAAGAGGTTTGTTGGTCCAATTACACCTACAATTATTTCTTTGAG
| | || || || | | | | | || ||| || ||| ||| | ||| | |||| || ||||||||||| |||| || | ||| |||||||||||||||||||| ||||| |||||||| |||| ||||| ||||| ||||||||||| || ||| ||||||| | || | || ||
gttgtgctccccctgtaggcatttatatcttctcctattgaatgtatatgataatatattcattactttgcttgctgtagattacattagtgctagtaatttcttactgataaactttataatt---atgtgaagGGCGAATGTGGTGTCATTGCCGGATGGTTTATTTGCCTATGTGTTACATTTATGGAAAGAGGTTTGTGGGCCCAGTTACACCAATTATATTGGAATTAAG
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 5
acaagttaccaataaattag-gcagcttttcaggttgattttatcttactgcaagcaggattttatttgttggt--gataaactttcaaatttt----tatct-atagGACGAATGTGGTGTCATTGCCGAATGGTGTATTTGCCCATGTCGTACATATATGGGAAGAGGTTTGTTGGTCCAATTACACCTACAATTATTTCTTTGAG
|| | |||| || |||| | | | | |||| | || |||| || | |||| ||| | | ||| | ||| | ||| | |||||||||||||| ||||||||||||||||| |||| ||||| |||||||||||||||||||||| ||| ||||| | | || ||
-----ctat-gttgcattaccatagtctttcgg--tagtctgctcttggttgctatgttgttacttttgctgatacgatacactattatggtttacaatgtcttacagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATCTATGGGAAGAGGTTTGTTGGTCGAATCACACCACTCGTGTTGGAATTAAG
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G023798_T02 (Zea mays), 3'ss of exon 3
acaagttaccaataaattaggcagcttttcaggttgattttatcttactgcaagcaggattttatttgttg-gtgataaactttcaaatttt----tatct-atagGACGAATGTGGTGTCATTGCCGAATGGTGTATTTGCCCATGTCGTACATATATGGGAAGAGGTTTGTTGGTCCAATTACACCTACAATTATTTCTTTGAG
|||||| || | || |||||| | | | | | | | | ||| | ||||| |||| ||| | ||| ||| | |||||||||||||| ||||||||||||||||| |||| ||||| |||||||||||||||||||| | ||| ||||| | | || ||
----attacca-taggtcca-tagtctttcagtagtgtgctcttggtttctttgttgtttcctttttctcatatgatacgcttttgtggtttacaatgtcttgcagGGAGGATGTGGTGTCATTGTCGAATGGTGTATTTGCCAATGTGCTACATTTATGGGAAGAGGTTTGTTGGCCGAATCACACCACTTCTGTTGGAATTAAG
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G341010_T01 (Zea mays), 3'ss of exon 5
acaagttaccaataaat-taggcagcttttcaggttgat-tttatcttactgcaagcaggattttatt-tgttggtgataaactttcaaatttttatctatagGACGAATGTGGTGTCATTGCCGAATGGTGTATTTGCCCATGTCGTACATATATGGGAAGAGGTTTGTTGGTCCAATTACACCTACAATTATTTCTTTGAG
| || ||| || || | | | | | || | ||| | | | | | |||| || | |||| | | || |||| || |||||||||||||||||| |||||| ||||||||||| ||| | |||||||||||||||||||| | |||||||| | | | ||
---atatatatatatatatatatatatatatatatatatatatatatatatatatatatatatatattatgacgatgattattcgctcacaaaataatcgtagGTCGCATGTGGTGTCATTGCCGAGCGGTGTACTTGCCCATGTCTTACGTCTATGGGAAGAGGTTTGTTGGGCGTATTACACCACTTGTCTTGGAACTCAG
upper sequence: Vv09s0018g00630.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G369401_T01 (Zea mays), 3'ss of exon 3
acaagttac-caataaattaggcagcttttcaggttgattttatcttactgcaagcaggattttatttgttggtgataaactttcaaatttttatctatagGACGAATGTGGTGTCATTGCCGAATGGTGTATTTGCCCATGTCGTACATATATGGGAAGAGGTTTGTTGGTCCAATTACACCTACAATTATTTCTTTGAG
||| | || || | | | ||| | | || | | | | ||| || ||| | || | | | | ||| | ||| ||||||| || |||||||||||||||||||||||||||| ||||| ||||| | |||||| ||||| ||||| ||||| | | || || ||
acatctaacatgatgagtgtaaaaattttacggtgagaactaaataagcccttactaggccattcttttctaatgcaataatgattcaccactat-tgcagGTCGAATGTCTTGCTATTGCCGAATGGTGTATTTGCCCATGTCTTACATTTATGGTAGGAGGTTCGTTGGCCCAATAACACCACTAGTAATGGAATTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactgcaagcaggattttatttgttggtgataaactttcaaatttttatctatagGACGAATGTGGTGTCATTGCCGAATGGTGTATTTGCCCATGTCGTACATATATGGGAAGAGGTTTGTTGGTCCAATTACACCTACAATTATTTCTTTGAG
atcttac putative branch site (score: 3)
tttttatct putative PPT
tgataaactttcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaagttaccaataaattaggcagcttttcaggttgattttatcttactgcaagcaggattttatttgttggtgataaactttcaaatttttatctatagGACGAATGTGGTGTCATTGCCGAATGGTGTATTTGCCCATGTCGTACATATATGGGAAGAGGTTTGTTGGTCCAATTACACCTACAATTATTTCTTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - aataaat
- - - - - - - - - - - - - - - - - - - - - - - - -gcaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gataaac