Sequence
atgc intronic sequence ATGC exonic sequence...ggattttgcatttttatacaactgtttctattccataaatgctacaattttttatttatttttaatatctttttaagttgtgtttttcattcttgtgcagGACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAACCAGCTCTACTCTACATTGTTCCATTCACACTCG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os06g51430.1 (Oryza sativa), 3'ss of exon 12
--------------------------------------------ggattttgcattt--ttatacaactgtttctattccataaatgc-tacaattttttatttatttttaatatctttttaagttgtgtttttcattcttgtgcagGACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAACCAGCTCTACTCTACATTGTTCCATTCACACTCG
| |||||| | | || | || | || | || | || | |||| | | | | | | || | || |||| | | ||||||||| || |||||||| ||||||||| | ||||| || ||||||||||| || || |||||||| || || |||||||| |
gtaagttacagcgctggtccacgcaactattacttgagacaaaaaaaagaggcatttatctgtgcatccgtcttatttaagctattgtattaaagctattatgtgctgtgaggaattaattt-gctgaactttttgcccacatcaagGACTCCTTATTACATATGTCGCCTTGAACCTTATGGACGGACATGGCCAACCTGCACTTCTCTACATAGTGCCCTTCACACTTG
upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 12
ggattttgcatttttatacaactgtttctattccataaatgctacaattttttatttatttttaatatctttttaagttgtgtttttca--ttcttgtgcagGACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAACCAGCTCTACTCTACATTGTTCCATTCACACTCG
| | || | ||| || | || | || ||| || | ||| || || | | ||| || || ||| | ||| || | ||||| ||||| ||||||||| | |||||||| ||||| ||||||||||| || |||||||| || || || || |
atacgtgaacaattgaaacatctaacaaaac-ccgtgcg-gcaacatgttggtgttttttacctgtagtctgacatactgtattcttttgccccttctttagGTCTTATGATCACGTATGTTGCCTTGAACCTTATGGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG
upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 10
ggattttgcatttttatacaactgtttctattccataaatgctacaattttttat--ttatttttaatatctttttaagttgtgtttttcattcttgtgcagGACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAACCAGCTCTACTCTACATTGTTCCATTCACACTCG
|| |||| | | || || |||| | || | || || || | ||| | | | | ||||||| || ||||||||||| || ||||| |||||||||||||||| ||||| || || | ||||| || || ||||| || |
-----------------gtaa--gttttgagtggatgaacgctaatgcagcagaagattggaaacattaactggctatttcttgtgtggccacataat-cagGACTTCTAATCACATATGTTGCGCTGAACCTGATGGATGGGCATGGACAACCTGCCCTTTTGTACATCGTGCCCTTCACTCTTG
upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G165351_T02 (Zea mays), 3'ss of exon 10
ggattttgcatttttatacaactgtttctattccataaatgctacaattttttat--ttatttttaatatctttttaagttgtgtttttcattcttgtgcagGACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAACCAGCTCTACTCTACATTGTTCCATTCACACTCG----------------
|| |||| | | || || |||| | || | || || || | ||| | | | | ||||||| || ||||||||||| || ||||| |||||||||||||||| ||||| || || | ||||| || || ||||| || |
-----------------gtaa--gttttgagtggatgaacgctaatgcagcagaagattggaaacattaactggctatttcttgtgtggccacataat-cagGACTTCTAATCACATATGTTGCGCTGAACCTGATGGATGGGCATGGACAACCTGCCCTTTTGTACATCGTGCCCTTCACTCTTGGTAATGATGTGTGTTT
upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA03G01100.2 (Glycine max), 3'ss of exon 10
ggattttgcatttttatacaactgtttctattccataaatgctacaattttttat-----ttatttttaatat--ctttttaagttgtgtttttcattcttgt--gcagGACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAACCAGCTCTACTCTACATTGTTCCATTCACACTCG----------------
|| || | | || |||| | ||| | ||| | | | | | || | |||| | | || ||| || | ||||| |||||||||||||||||||| ||||||||||||||||||||||| || |||||| | || || || || ||||| ||||| |
--------cagttctgtttgcttgcttcttccctatag-tcctatcttcacctgtggaagtggctgttggctttgtcctttacatcattccttgaatttttatctgcagGTCTCCTCATCACATATGTGGCTTTGAACTTGATGGATGGGCATGGTCAGCCAGCTTTGCTTTATATAGTCCCATTTACACTTGGCAAGTATAATTAATC
upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA03G01100.1 (Glycine max), 3'ss of exon 12
ggattttgcatttttatacaactgtttctattccataaatgctacaattttttat-----ttatttttaatat--ctttttaagttgtgtttttcattcttgt--gcagGACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAACCAGCTCTACTCTACATTGTTCCATTCACACTCG
|| || | | || |||| | ||| | ||| | | | | | || | |||| | | || ||| || | ||||| |||||||||||||||||||| ||||||||||||||||||||||| || |||||| | || || || || ||||| ||||| |
--------cagttctgtttgcttgcttcttccctatag-tcctatcttcacctgtggaagtggctgttggctttgtcctttacatcattccttgaatttttatctgcagGTCTCCTCATCACATATGTGGCTTTGAACTTGATGGATGGGCATGGTCAGCCAGCTTTGCTTTATATAGTCCCATTTACACTTG
upper sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G07610.1 (Glycine max), 3'ss of exon 13
ggattttgcatttttatacaactgtttctattccataa----atgctacaattttttatttatttttaatatctttttaagttgtgtttttcattct--tgtgcagGACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAACCAGCTCTACTCTACATTGTTCCATTCACACTCG
|||| | | | || |||| | | ||| || | ||| | | | | | | |||| | | || ||| | | || ||| |||||||||||||||||||| ||||||||||||||||||||||| || |||||| | || || || || ||||| ||||| |
------tgcaaatctgttagcttgcttctttcctatattcctatcttcaaatgtcgaagtgactgggctttgtcctttacatcattccttgaattttgatctgtagGTCTCCTCATCACATATGTGGCTTTGAACTTGATGGATGGGCATGGTCAGCCAGCTTTGCTTTATATAGTCCCATTTACACTAGMapped 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|110401255|gb|EC967858.1|EC967858EST: GAGTCTCCGAGCAGGATACTTTGTGTGGGCCATGACTGCTTATGGTCTAG GACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAAC
genomic: GAGTCTCCGAGCAGGATACTTTGTGTGGGCCATGACTGCTTATGGTCTAGgtatggagga ... tcttgtgcagGACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAAC
EST:
gi|110369217|gb|EC933370.1|EC933370EST: GAGTCTCCGAGCAGGATACTTTGTGTGGGCCATGACTGCTTATGGTCTAG GACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAAC
genomic: GAGTCTCCGAGCAGGATACTTTGTGTGGGCCATGACTGCTTATGGTCTAGgtatggagga ... tcttgtgcagGACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattttttatttatttttaatatctttttaagttgtgtttttcattcttgtgcagGACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAACCAGCTCTACTCTACATTGTTCCATTCACACTCG
ttttaat putative branch site (score: 3)
tgtttttcattctt putative PPT
tttatttatttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggattttgcatttttatacaactgtttctattccataaatgctacaattttttatttatttttaatatctttttaagttgtgtttttcattcttgtgcagGACTCCTCATCACATATGTGGCCTTGAACTTGATGGATGGGCATGGCCAACCAGCTCTACTCTACATTGTTCCATTCACACTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- -ttttgca
- - - - - - - - - - -ctgtttc
- - - - - - - - - - - - - - - - ccataaa
- - - - - - - - - - - - - - - - - - - -tgctaca