Sequence
atgc intronic sequence ATGC exonic sequence...aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattgataactgatttacttttctttctgggctgaactgttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattgataactgatttacttttctttctgggctgaact--------gttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA
| | | |||| | || ||||| | || | || ||||||| | | || | | || ||| || | | | |||| | |||||| | | ||||| || || ||||| |||||||| |||||||||||||| |||||||| ||||||||||||||||||||||| ||||| |
------cgagtattttttggatgccatgtttc--atttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaattgccagGAGGCGGCTGGTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g22670.1 (Oryza sativa), 3'ss of exon 4
aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattgataactgatttacttttctttctgggctgaactgttcaaaacg--aatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA
| | || | ||| | || | || || | | | || | | | ||| || | | | || ||| | | |||| || ||||| | | | | |||||| |||||||| ||||| |||||||| ||||| || ||||||||||||||||| |||||||||||||
--tcttttgaattttcaaactcattttgtttggtagatttatatacaacattctcttcatgtgatatttttatgcatttgattaatcttaactgcacaccagGATGATGCTGGAGCACCAGCCTCACTTCCAAAGCATAATAAAGGTTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAATGCTTTCAAGCAA
upper sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G104246_T01 (Zea mays), 3'ss of exon 3
aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattga-taactgatttacttttctttctgggctgaact---gttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA
| | | | | | || | || ||||| ||| || | | | | || | | | | ||| | || | || || | |||||| | | || | | |||| || || || ||||| |||||||| ||||| |||||||| ||||| |||||||||||||||||||||||||| ||||| |
---ctatcaaatac-tgaaattatgtcattattgcatttaatttggaccaagttattgtgctgccatgacatgtggcattaattctagtccatgaaattgctagGAGGTGTCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGCCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G059678_T01 (Zea mays), 3'ss of exon 3
aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattgata-actgatttacttttctttctgggctgaactgttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA
|| ||| | | | | | || |||| || || | ||| || | | | | ||| | |||| | | || | | |||| || || || ||||| |||||||| ||||| |||||||| ||||| || ||||||||||||||||||||||| ||||| |
-atcaattacaggcattatatcattattgcatttcatttcggccatgttattgtgctgccttgacacgtcacattaattctagtccatgaaattttgccagGAGGTGCCTAGTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA
upper sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G342588_T01 (Zea mays), 3'ss of exon 3
aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattgataactgatttac-ttttctttctgggctgaactgttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA---
| | | | || || | | ||| || || || | || ||| | || || | | || || | | | || || ||| | || ||||| | | || | |||||| |||||||| || ||||||||||| |||||||| || ||||| |||||||| || |||||||| |
attttatgtttgatttacttctatttgatt--cagttgaaatatttctttatatgtttcatatattgtttagctaatcttagcaacttgaaccgg--ctatcagGATGCTGGAGCACTACCTTCACATCCAAAGCATAATAAAGGTTGTCACTGCAAGAAGTCAGGTTGTCTAAAGAAATACTGTGAATGTTTTCAAGCGAATA
upper sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G388148_T01 (Zea mays), 3'ss of exon 3
---aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattgataactgatttacttttctttctgggctgaactgttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA
||| | |||| | | | | | |||| | | | | | ||| | | | | | | || || || ||||| | |||| |||||| | || | ||||||| ||||||| || || |||||||| ||||| ||||| |||||||||||||| |||| |||||||
cttaatccat-atttgtttgt-gctatttcccaaccaatacactctagtttctttgcttgagctgcatgtgaccactgcactacttgactaatgtctat-tagGATAATTCTGGAGCAGTCCCTCTCGTAGCAAAGCACCATAAAGGTTGTCATTGCAAGAAGTCAGGATGCCTAAAGAAGTACTGTGAATGCTACCAAGCAA
upper sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G08780.1 (Glycine max), 3'ss of exon 6
-----------------------------aatgtgttatttccctaaag-atg-tgaaatta--tcaattttcatg-aatattgataactgatttacttttcttt-----ctgggctgaactgt-------tcaaaa--cgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA------
| |||||||| | | | ||| || ||| |||| ||| || || | | |||| | | ||| | | | | | | ||| | ||| | | | | ||| | || | | | | | |||||||||||||||||||| ||||||||||||||||||||||| |||||||| ||||||||||| ||||| |
gtttgtaattcaatttcaactccctcaaacaggtgttattgctttttggcatgatgcttttaagtcaagttttttgtgatgatacttactgttctgggtttatctgatattttagttaacttgtggtgcatttaaatatcttgtttgaacacagGAATGTGAAATTCAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGTTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
upper sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G08670.1 (Glycine max), 3'ss of exon 3
-----------------------------aatgtgttatttccctaaagatgtgaaattatcaa------ttttcatga--atattgataact---gatttactt----ttctttctgggctgaactgttcaaaa-cgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA------
|||||||||| | | ||| | | || |||| ||| ||| | | | | |||| | || | | || | || || | | | | | ||| | || | | | | |||||||||||||||||||| ||||||||||||||||| ||||| |||||||| ||||||||||| ||||| |
gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttgg-catgaggcttttaagccaagtttttgtgatgatacttactgttctgggtttagctgatattgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
upper sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G25790.1 (Arabidopsis thaliana), 3'ss of exon 3
aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattgataactgatttacttttctttctgggctgaactgttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA
||||| || | | || ||| | | || ||| || ||| || | | | | || | ||| | ||||| | | | |||| | | |||||||||| |||||||||||||||| ||||||||| || |||||||||||||||||||| | || || |
------------------gtttgtgatcttgttactt-----gaaaa---aaaaaagatgtaactttagggcttgatggtagt-tttataact--tgtagGAGAATGTGCAGCAAGTGTTGCTTATTGGAAAGCACAGCAAAGGATGCCACTGCAGGAAATCAGGATGTCTCAAGAAGTACTGTGAGTGTTACCAGGCGA
upper sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattgataactgatttacttttct---ttctgggctgaactgttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA
| || || || | | || |||| ||| | ||| || | | | || || || | | | | | |||| || ||||| | ||||||| ||| || ||||| |||||||| || ||||||||||| || |||||||||||||| || || ||||| ||||| |
---tcatgtattttctgtagtaccaaggtgttccttttttatggacatttcccctcaatctgggtcagtggatttcggaactaatagaactttattattgcagGAGGATGCTGGAGAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA
upper sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 5
aatgtgttatttccctaaag--atgtgaaattatcaattttcatgaatattgataactgatttacttttctttctgggctgaactgttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA
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--cgtattccttctgttgtaccaaattatattccatagtttcattatttttcttaacctgggcgagtggttgacgaaactgatggcatcttggttattgcagGAGGATGTTGGAGAGCATCCTCTGGCGGGCAAGCACAACAAAGGATGCCACTGTAAAAAGTCGGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCCAMapped 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|161721389|gb|FC070429.1|FC070429EST: CATTCAGACCAAAGATTGCTAATAGTCCACAAGGATCTCATGATGGTGGG GAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCAC
genomic: CATTCAGACCAAAGATTGCTAATAGTCCACATGGATCTCATGATGGTGGGgtgagtattt ... acgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgataactgatttacttttctttctgggctgaactgttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA
atttacttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgtgttatttccctaaagatgtgaaattatcaattttcatgaatattgataactgatttacttttctttctgggctgaactgttcaaaacgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - ccctaaa
- - - - - - - - - - - - gaaatta
- - - - - - - - - - - - - - - - - - - -catgaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggctga