Sequence
atgc intronic sequence ATGC exonic sequence...gtttcatatgtttgttacatataaacacactcctttgcctatctaacaggaaaaaaattatgtcttaaacattcttgttgttcatgagttgcttttgcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 3'ss of exon 2
-------------------------------gtttcatatgtttgttacat-ataaacacactcctt-tgcctatctaacaggaaaaa-aattatgtcttaa-------acattcttgt-tgttcatgagttgcttttgcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
|| ||| ||| | || || ||| | | || || | | | | ||| || |||||| ||| ||| | |||| || | ||||||||||| || ||||| || ||||| ||||| || ||||| |||||||||| ||||| |||||||| || || ||||| || |||||||| |||||||
gtttttctcttaagatctttgcatgcttttgattgtctatattttgcatattgtagacatagtttttacttctctttggaattatttctaataatctcttaacctgggagcatacttaagttttcactgtttcatggaacagATAGATGCAGCTATAAATTCAGGAAACTCTGGGGGCCCTGCTTTTAATGATAAGGGCAAGTGTGTGGGCATAGCTTTTCAATCTCTTAAACACGAAGATG
upper sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 2
gtttcatatgtttgttacatataaacacactcctttgc-ctatctaacaggaaaa-aaattatgtcttaaacattcttgttgttcatgagttgcttttg-cagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
||||| | | ||| || || | | ||||| |||| || | || | | | | |||| | | || | | | | | ||||||||||| || || ||||| |||||||| ||||| || || ||||||| | ||||||||||| ||||| || ||||| || || |||||||||||||
-gttcattttctccccaca-attctcatttagaatagtattatctgtgaggataacatgttgagaaatcataagtcttttaacttttggggttttatggacagATAGATGCAGCTATTAACTCAGGAAATTCAGGTGGCCCAGCTTTTAATGACAGGGGCAAATGTGTTGGTATAGCTTTTCAATCTCTCAAACATGAAGATG
upper sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G144501_T02 (Zea mays), 3'ss of exon 2
---------------------------gtttcatatgt-ttgttacatataaacacactccttt------gcctatctaacaggaaaaaa---attatgt-cttaaacattcttgttgttcatgagttgctt---ttgcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
|||| || ||| ||| | | | | ||||| |||| || |||| | |||| | | | | | ||| | | |||||||||| || || || || |||||||| ||||| || || ||||||||| |||||||||||| ||||| |||||||| || ||||||||||||||||
gtacctttcccccctgaaattataataacttcaaataaacctttatataaagatggatgttgcaagtgaagtaaatctattgagaaataataacttatctgcttaccggcatgtctaatacgggccttgtcttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGTCCAGCTTTTAATGATAGAGGCAAATGTGTCGGTATAGCATTTCAATCTCTTAAACATGAAGATG
upper sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM5G877597_T02 (Zea mays), 3'ss of exon 2
--------------------------gtttcatatgtttgttacatataaacacactcctttgcctatctaacaggaa-----aaaaattatgtcttaaacattctt----gttgttcatgagttgctttt---gcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
|||| || | || |||||| | | || || | | | | | |||| ||| |||| || || | || ||| || |||||||||| || || || || |||||||| ||||| || || ||||||||| || |||||||| ||||| || |||||||| ||||||||||||||||
gtacatttttttctgaaattatgataacttcaaataaatctttt-tataaagatagatgtt-gcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaataccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
upper sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 2
----------------------------gtttcatatgt-ttgttacatataaacacactcctttgcctatctaacagga--aaaaaattatgtcttaaacattc-ttgttgttcatga----------gttgcttttgcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
|||| || | || ||| | | | | | |||| | ||| ||| |||| || | || | | || || |||||||||| || || || || |||||||| ||||| || || ||||||||| || |||||||| ||||| || |||||||| ||||||||||||||||
gtacattttttttcctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaactattttgagaaaccatgacttatcggctcaccgacgtgtctaatacgggccttgtcttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
upper sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G165969_T01 (Zea mays), 3'ss of exon 3
----------gtttcat-atgtttgttacatataaacacactcctttgcctatctaacag-gaaaaaaattatgtct-taaacattcttgttgttcatgagttgcttttg--cagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
|| || || || | | | || | ||||||| | || ||| | | | | | | | |||||| | || || | ||||||||||| || ||||| || |||||||| || || ||||| | |||||||| || |||||||| ||||| || || || || ||||||||||||||||
gtattaacgtattgtattatattctgcatacttttacttatagatttgccttttatacgttgaactatgccacacttatgtaaacttctgttgtctgtttattactcataaacagATAGATGCAGCTATAAATTCAGGAAATTCAGGGGGGCCTGCTTTCAATGATAAGGGAAAATGTGTTGGTATAGCTTTCCAATCTCTTAAACATGAAGATG
upper sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G015959_T01 (Zea mays), 3'ss of exon 2
---------------------------gtttcatatgtttgttacatataaacacactcctttgcctatctaacaggaa-----aaaaattatgtcttaaacattc-ttgttgttcatga----------gttgcttttgcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
|||| || | || |||||| | | || || | | | | | |||| ||| |||| || | || | | || || |||||||||| || || || || |||||||| ||||| || | ||||||||| || |||||||| ||||| || |||||||| ||||||||||||||||
gtacattttttctctaaaattatgataacttcaaataaatctttt-tataaagatagatgtt-gcaagtgaagtaaatattttgagaaatcatgacttatcggctcaccgacgtgtctaatacgggccttgtcttgttaatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAACTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
upper sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 2
gtttcatatgttt---gttacatataaacacactcctttgcctatctaacaggaaaaaaattatgtcttaaacattcttgttgttcatgagttgcttttgcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
|| |||| ||| | || | ||| | | || | | | | | ||| | ||||| || | || | | |||||||||||||||||| ||||| ||||| ||||||||||||||||| | |||||||| || ||||| || || || ||||| ||||| ||||||||||||||||
gtaacataggttctaagctatcccttttcacttttccatgtatgccccgcttgtccatttatatatgttaaattgaagcgtctctt-cgaat--cctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|161708433|gb|FC056139.1|FC056139EST: TGGAGATATTATCTTATGTTCATGGTTCAACTGAGCTTCTTGGTCTTCAG ATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGAT
genomic: TGGAGATATTATCTTATGTTCATGGTTCAACTGAGCTTCTTGGTCTTCAGgttatccatt ... gcttttgcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGAT
EST:
gi|34546836|gb|CF515068.1|CF515068EST: TGGAGATATTATCTTATGTCCATGGTTCAACTGAGCTTCTTGGTCTTCAG ATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGAT
genomic: TGGAGATATTATCTTATGTTCATGGTTCAACTGAGCTTCTTGGTCTTCAGgttatccatt ... gcttttgcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaggaaaaaaattatgtcttaaacattcttgttgttcatgagttgcttttgcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
atctaac putative branch site (score: 2)
ttgctttt putative PPT
aaaaaaattatgtctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttcatatgtttgttacatataaacacactcctttgcctatctaacaggaaaaaaattatgtcttaaacattcttgttgttcatgagttgcttttgcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - -cacactc
- - - - - - - - - - - - - - - - - -tgcctat
- - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgagt