Sequence
atgc intronic sequence ATGC exonic sequencegtcagtccccacttattctgatgtattaagccctgttgtgatatggaacattgtgatcagaactcctaaactgtgtataattttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g40840.2 (Oryza sativa), 3'ss of exon 8
gtcagtccccacttattctgatgtattaagccctgttgtgatatggaacattgtgatcagaactcctaaactgtgtataattttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG
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------------gtttgatatcttgtcatgcatatttttcctttcttttaccttagcctatgttcctaa-ccataaaaaacctt--tagGGGGAAGCATTGTTTCAAACACATGAGAACCTTGAGCACTTAGCAATGATGGAGAGGGTTTTGGGTCCACTCCCAGAACACATGATAAGGAAAGCCAG
upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G366935_T09 (Zea mays), 3'ss of exon 8
gtcagtccccacttattctgatgtattaagccctgttgtgatatggaacattgtgatcagaactcctaaactgtgtataattttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG
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gttagatctc---tgctcagttttctca--cttttttttccta-gtaccagtctggtaattatttttctaacat-cacactttttttagGGGGAAGCATTGTTTCAGACACATGAGAATCTGGAACACCTAGCAATGATGGAGAGAGTTTTGGGACCTCTACCAGAGCATATGATACGGAAATCAAG
upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 7
gtcagtccccacttattctgatgtattaagccctgttgtgatatggaacattgtgatcagaactcctaaactgtgtataattttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG
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gttagatctc-----ttcacacacttta----tttttctagtaccagtc-tggtaatt-gttttcctaacat---cacattttt--tagGGGGAAGCATTGTTTCAGACACACGAGAATCTGGAACACCTAGCAATGATGGAGAGGGTTTTGGGACCTCTACCAGAGGATATGATACGGAAAGCAAG
upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
gtcagtcccc---acttattctgatgtattaagccctgttgtgatatggaacattgtgatcagaactcctaaactgtgtataattttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG
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gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaacaactagtcttagtgttctaaa-tgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA
upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S100_121V6.1 (Physcomitrella patens), 3'ss of exon 11
------------gtcagtccccacttattctgatgtattaagccctgttgtgatatggaacattgtga---tcagaactcctaaactgtgtataattttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG
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tccctcgaagaaggctactgtagctgtatctactacacatgacggtagccgtacatggatcaatatgtcttttaataactttattcattgtttgtttt----agGGTGATGCGCTGTTTCAGACTCATGAGAACTTGGAGCATTTGGCTATGATGGAGCGGGTTTTAGGTCCCATTCCCGTTCACATGATAAGGAGGGCAGA
upper sequence: Vv04s0008g04220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S132_58V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------------------------------------------gtcagtccccacttat-tctgatgtattaagccctgttgtga---tatggaa--cattgtgatcagaactcctaaactgt-gtata-attttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG
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gtatgggattcctatcgccttcctttctcttttatattcctctattatccagtaattccctatactttctcttcaaacttgtaaatttgagaaaatctttgatgtcatagtttttcatgcgaagatgttgaaaccaatgtaaatgtttttcagtggttacagtatttgctatggcagGGTGATGCATTGTTTCAGACTCACGAGAATTTGGAGCATTTGGCTATGATGGAACGAGTCTTAGGTCCTATTCCTGTACACATGATCAAGAGGGCAGAMapped 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|110378511|gb|EC943648.1|EC943648EST: ATCCATGTGATTTATGGAGTGTTGGTTGCATACTAGTGGAACTTTGTGTG GGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATG
genomic: ATCCATGTGATTTATGGAGTGTTGGTTGCATACTAGTGGAACTTTGTGTGgtcagtcccc ... attttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgtgatatggaacattgtgatcagaactcctaaactgtgtataattttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG
tcctaaa putative branch site (score: 2)
tgtataatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtccccacttattctgatgtattaagccctgttgtgatatggaacattgtgatcagaactcctaaactgtgtataattttgacagGGTGAAGCATTATTTCAGACACATGAGAACTTGGAGCATTTGGCCATGATGGAGAGGGTGTTGGGACCTCTGCCAGAGCATATGATTCGGAGGGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA