Sequence
atgc intronic sequence ATGC exonic sequencegtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os02g50320.2 (Oryza sativa), 3'ss of exon 5
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattt-tgttttggattttttttgtgtaatc--ttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
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------------------------------------------------------tgtcattctcccgtacgtctgtattttgtaactcctgtatctccttgatggcatttttcaatttttctcaaactgaattgattatctttctggattaaagGAAGAAAATAAGATCTTGGACAGGCTGCACCGCCAAAAAGTTGCTGAAGTAGAAAAGCTTAGTCAAACTGTAAGAGAGCTGGAAGAGGCTGTTCTTGCTG
upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g14080.1 (Oryza sativa), 3'ss of exon 5
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttcctttgtttaatta-gcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
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--------------------------------------------------------gtatgtactgtgtt-cctagttgtaggataaatttacttggacatgcct-gtggaactacacaagtgctcaattgtttg--ctttatgcattgcagGAAGAAAATAAAATATTGGACAAGTTACAACGCCAAAAGGTTGCAGAAGTTAAAAAACTTAGCCTAACCGTGAAAGAACTGGAAGAGGCTGTTCTTCGAG
upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G039325_T01 (Zea mays), 3'ss of exon 5
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttccttt--gtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
|| | | || |||| | | ||| | || || || | | | | || || |||||| | || || || |||| | |||||||||||||||| || |||||| |||||||||||||| ||||||| |||||||| || | ||||||||| |||||| | ||||| |||||||| |
----------------------------------------gtaag-tgggtgcatgcagtttattccct-atcatgaga-agacaatagacaacaacttggcattccaattgaattagtttagtgctaattgattgatttgtttgcactgcagGAAGAAAATAAAATCTTAGATAAGCTGCATCGCCAAAAGATTGCAGAAGTTGAAAAGCTTAGCCAAACTGTGAGGGAGTTGGAAGAAGCTGTTCTTCAAG
upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G008556_T01 (Zea mays), 3'ss of exon 5
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
||| ||| ||| |||| |||| || || | | || | || ||| | || ||| | | | | | | || | || | | |||| || | |||| | | | | ||||| || |||||||||||||||| || || ||| |||||||||||||| ||||||| |||||||| || | ||||||||| || ||| | |||||||||||||| |
gtaa-gtgggtgc--atgcagttt-attctctatcatga----------aaacacaataacttggcattccaattgaatagtttagtgcctaattgattattattattattattattatta--ttat-tatta--ttattttgcattgcagGAAGAAAATAAAATCTTAGACAAGCTGCATCGCCAAAAGATTGCAGAAGTTGAAAAGCTGAGCCAAACTGTGAGAGAGTTGGAAGAGGCTGTTCTTCAAG
upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 1
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtat--actagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
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--------------------------------------------gtacgcgacagtggagatattcattgacactagt---aactttaccagcttgtttgcccataagctaac-------agtatatgaggctt-tcctgttgcaccaaacagGAAGAGAACAAAATCTTGGATAGAATGCACCGCCAGAAAGTTGCTGAGGTTGAAAAGCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTG
upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 5
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
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-----------------------------------gtattgcaatcttgtatgat----tattctctctcctggtgtgtgagaatcataatatgtaa-cttctatctctgactttgc-----------catcaacttcctc--------agGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAG
upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 5
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
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-----------------------------------gtattgcaatcttgtatgat----tattctctctccaggtgtgtgagaaccataatatgtaacttctatcttcggactttgc-----------catcaacttcctc--------agGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAG
upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 5
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
| | | || || | ||| | ||| | | | | || | |||||| ||| | | ||| || || ||| ||| | | | |||||||||||||||||||||||| || |||||| | | ||||| |||||||||||||| || |||||||| || || || || ||||||||||| || || |
-----------------------------------gtatttgcaattt----cgtatggtgtttccctctccaagtatgccagccttaataatgtaat-ttcttatatttggtt--------ttggtatc----atcatcacctctcctagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 5
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
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--------------------------------------------------------gtatttgcaattttgtattgtgtt---tctctctcaagtatgccagacataataatgtaatttctgacatttggtttcatcatcacctctcccagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
upper sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G01750.1 (Arabidopsis thaliana), 3'ss of exon 6
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcat-attatcttttcttttattt---tgttttggattttttttgtgtaatcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
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---------------------------------------------------gtatcactttcgcctcctttacccagcagtactataaattcctggatctctctccttcgttttcgtgagcatgc-cttgtttatcga----ttgttcaaattagGAAGAGAACAGAATTTTGGACAAGTTGCACAGACAAAAGGTTGCAGAAGTTGAAAAGTTTACCCAGACCGTACGGGAGCTTGAAGAAGCTGTTCTTGCTGMapped 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|161719957|gb|FC067712.1|FC067712EST: ATCTTCAGAATAAGAACCAAGAGCTGATGAAACAAATAGAAATTTGCCAG GAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTT
genomic: ATCTTCAGAATAAGAACCAAGAGCTGATGAAACAAATAGAAATTTGCCAGgtattgtgat ... tgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
gtttaat putative branch site (score: 4)
tccttttgt putative PPT
tttatatgtcaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT