Sequence
atgc intronic sequence ATGC exonic sequence...tagccatagataaatattgctctgttctgtttgctattttcgtttttgatcagatttctgtttgctatattcctaactatacacactttatcttttttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g53195.1 (Oryza sativa), 3'ss of exon 2
----------tagccatagataaat--attgctctgttctgtttgctattttcgtttttgatcagatttctgt-ttgctatattc-------ctaactatacacactttatctttttt-agGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG
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gtaatatgtgatgcagtttatggcctaattgtaatgatataggttcaatgatcccttgaagtgcatttcaaatgttgtgaaattcttccccactggttattctaatgtggtttctttccagGTTGTTCTTCTAGAATCTCGTGACAGGATAGGTGGTAGAATTCACACTGATTACTCTTTTGGCTTTCCTGTTGATCTGGGAGCATCCTG
upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G396856_T02 (Zea mays), 3'ss of exon 3
----tagccatagataaatattgctctgttc---tgtt-----tgctattttcgtt-tttgatcagatttct--gtttgctatattcctaactatacacacttt-atcttttttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG
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gtatttttcagtgttacttcttgtcatgtttgtgtgttggtgatgcaatcatatttatttgagaaaaatggaaagatccttttgtgatgcatttcggttgctctgatgcatttcagGTTATTCTTCTGGAATCTCGTGATAGAATTGGTGGCAGAGTTCACACTGACTACTCTTTTGGGTTTCCAGTCGATTTGGGAGCATCTTG
upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G14620.1 (Glycine max), 3'ss of exon 2
--tagccatagataaatattgctctgttctgtttgctattt--tcgtttttgatcagatttctgtttgctatattcctaactatacacactttatcttttttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG
| | || || ||| || | || ||| | | | |||| || | ||| || | || | | | | || | |||||||||| || || || | |||||||||||||| || |||| |||||||||||||||||||||||||||||||||||||||||||
gaaacttgaacctacatgttgttcgaagccaattattatgcaattatgcatttccagagttgaggg-actaaatggttc-ctttgtttataat-ttttggtcaGGTTGTTCTCTTAGAGTCAAGGGATAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCAT-
upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G41570.3 (Glycine max), 3'ss of exon 2
tagccatagataaatattgctctgttctgtttgctattttcgtttttgatcagatttctgtttgctatattcctaact---atacacactttatctttt--ttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG
|| | | || |||| |||| ||| ||| || | | | | || | || ||| ||| | | |||| |||| | |||||||||| || || || | || ||||||||||| || |||| |||||||||||||||||||||||||| ||| |||||||||||||
taacttt---caaggattgtggtgttgtgt--gctgcttaattgtaaacttgaacttacatggcctcaattattaaatggtgcctatgttttaatttttggtcagGTTGTTCTCTTAGAGTCAAGGGAAAGAATTGGTGGCCGAATTCACACTGATTACTCATTTGGTTTTCCTGTGGACATGGGAGCATCATG
upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G03610.2 (Glycine max), 3'ss of exon 2
tagccatagataaatattgctctgttctgtttgctattttcgtttttgatcagatttctgtttgctatattcctaactatacacactttatcttttttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG
| || | | ||| | | || || || ||||| | || | || | |||| || || ||||| | ||| | ||||| |||| | ||||| || || ||| ||||||| || |||| ||||| ||||||||||| ||||||||||||||||| ||||| ||
--gtattaaagtttttttgttttcccctcttgaacatacatacttttgtac---ttgttaatttatttatttgtataaat-tgtacttt-tatttgtcagGTTATTCTTCTAGAATCACGAGAAAGACTTGGTGGCCGAATTCACACTGACTACTCATTTGGCTTTCCTGTTGACCTGGGTGCATCGTG
upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G45140.1 (Glycine max), 3'ss of exon 2
tagccatagataaatattgctctgttctgtttgctattttcgtttttgatcagattt-ctgtttgctatattcctaactatacacactttatcttttttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG
|| | | | ||| | | || || || | | | || | || | |||| | || ||||| | ||| | ||||| |||| | ||||| || || ||| |||||| || |||| ||||||||||||||||| |||||||||||||| || ||||| ||
---gtattaa-agtttttgttttcccctcttgaacatacatacatacttttgtacttgttaatttatttatttgcataaat-tgtacttt-tatttgtcagGTTATTCTTCTAGAATCACGGGAAAGACCTGGTGGCCGAATTCACACTGATTACTCATTTGGCTTTCCTGTTGACCTTGGTGCATCGTG
upper sequence: Vv12s0028g01120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G43020.1 (Arabidopsis thaliana), 3'ss of exon 2
tagccatagataaatattgctctgttctgtttgctattttcgtttttgatcagatttctgtttgctatattcctaactatacacactttatcttttttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG
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------------gtttgtgatgtttcatgttttatacaatatatcctgat---agctgattttgatatctctttctcacggtgtggttcttggtgtttagGTTATGGTACTGGAGTCCCGTGACAGAATTGGTGGACGAGTTCACACTGATTACTCATTTGGTTTTCCTGTTGATCTTGGTGCATCATGMapped 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|110697943|gb|EE075393.1|EE075393EST: GTATGGCAGGCATTGCAGCTGCTCGTGCCCTTCATGATGCCTCATTTCGG GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGAT
genomic: GTATGGCAGGCATTGCAGCTGCTCGTGCCCTTCATGATGCCTCATTTCGGgtattcaaaa ... tcttttttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGAT
EST:
gi|30303658|gb|CB980452.1|CB980452EST: GTATGGCAGGCATTGCAGCTGCTCGTGCCCTTCATGATGCCTCATTTCGG GTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGAT
genomic: GTATGGCAGGCATTGCAGCTGCTCGTGCCCTTCATGATGCCTCATTTCGGgtattcaaaa ... tcttttttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatcagatttctgtttgctatattcctaactatacacactttatcttttttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG
tcctaac putative branch site (score: 1)
cactttatctttttt putative PPT
actttatctttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tagccatagataaatattgctctgttctgtttgctattttcgtttttgatcagatttctgtttgctatattcctaactatacacactttatcttttttagGTTGTTCTGTTGGAATCGCGTGATAGAATTGGTGGACGGGTTCATACTGATTACTCATTTGGTTTTCCTGTTGACCTGGGAGCATCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - -agataaa
- - - - - - - - - - - - - -tgtttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcctaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacacac