Sequence
atgc intronic sequence ATGC exonic sequence...ggtaatccgacaatatatggtttcttctttgatctaccaacatgttcaattgcgatgaatgggttattttcttgtgcacttaccatatatcatttgacagGTGTCGGGACCAGTTGTCGTCGCAGATGGAATGGCAGGGGCTGCTATGTATGAACTGGTCCGTGTTGGACATGACAACCTTATTGGAGAAATTATTCGGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 1
ggtaatccgacaatatatggt-ttcttctttgatctaccaacatgttcaattgcgatgaatgggttattttcttgtgcactt---accatatatcatttgacagGTGTCGGGACCAGTTGTCGTCGCAGATGGAATGGCAGGGGCTGCTATGTATGAACTGGTCCGTGTTGGACATGACAACCTTATTGGAGAAATTATTCGGT
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--atgcgcactagtaattgccctttttcttttgtatgatggcatgtttagctct--taatttcattgtgttgatgaacattattgatcgaatgggttgttttagGTCTCTGGACCTGTGGTTGTGGCTGATGGAATGGGAGGTGCTGCCATGTATGAACTCGTCCGTGTTGGGCACGATAATCTTATTGGAGAAATTATTCGTC
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 1
--------ggtaatccgacaatatatggtttcttctttgatctaccaacatgttcaattgcgatgaatgggttattttcttgtgcacttaccatatatcatttgacagGTGTCGGGACCAGTTGTCGTCGCAGATGGAATGGCAGGGGCTGCTATGTATGAACTGGTCCGTGTTGGACATGACAACCTTATTGGAGAAATTATTCGGT
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atgttgattgtctactattggcacatgatccatcatttcatccctctttttttttt-ttgtattgaacgaattgtttc-----gccttcatattgcattcttc--tagGTTTCTGGACCTGTGGTCGTGGCTGATGGAATGGGTGGTGCTGCCATGTATGAACTTGTCCGAGTTGGTAATGATAACCTCATTGGGGAAATTATTCGTC
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 1
ggtaatccgacaatata--tggtttcttct-ttgatctac-caacatgttcaattgcgatgaatgggttattttcttgtgcacttaccatatatcatttgacagGTGTCGGGACCAGTTGTCGTCGCAGATGGAATGGCAGGGGCTGCTATGTATGAACTGGTCCGTGTTGGACATGACAACCTTATTGGAGAAATTATTCGGT
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--ccatctgtttacaagagtgaaatcttctgctgatgttcgcactgcagttatgtatataacaagccccactttgattagccttgatgctgggttatt--gcagGTCTCTGGACCTGTGGTTGTGGCTGATGGAATGGGTGGTGCTGCCATGTATGAACTTGTTCGTGTCGGACATGATAACCTCATTGGGGAAATTATCCGTC
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 1
--ggtaatccgacaatatatggtttcttctttgatctaccaacatgttcaattgcgatgaatgggttattttcttgtgcacttaccatatatcatttgacagGTGTCGGGACCAGTTGTCGTCGCAGATGGAATGGCAGGGGCTGCTATGTATGAACTGGTCCGTGTTGGACATGACAACCTTATTGGAGAAATTATTCGGT
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tttttgctgttactgtaattcgttgagggtgtgatctact--tagttccatgttttaataactcttcattctcctcctcacatatattcccaattgaaacagGTATCAGGACCAGTCGTCGTTGCAGATGGCATGGCTGGGGCTGCTATGTATGAACTCGTGCGTGTTGGTCATGATAATCTCATTGGTGAAATTATTCGTC
upper sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 1
ggtaatccgacaatatatggtttcttctttgat-ctaccaacatgttcaattgcgatga-atgggttattttcttgtgcact----taccatatatcatttga--cagGTGTCGGGACCAGTTGTCGTCGCAGATGGAATGGCAGGGGCTGCTATGTATGAACTGGTCCGTGTTGGACATGACAACCTTATTGGAGAAATTATTCGGT
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--------aacattttatttacttttttcctatgttgaggatgtgatccacttaattaataccatttactttcatgtatgctaaattatgttttcccaattaaaacagGTTTCAGGACCCGTCGTCGTTGCGGATGGCATGGCTGGTGCTGCTATGTATGAACTCGTGCGTGTTGGTCATGATAATCTCATTGGTGAAATTATTCGTCMapped 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|161718002|gb|FC067562.1|FC067562EST: CCACGTTCGAGGACTCGGAGAAGGAAAGCGAGTACGGTTACGTTCGCAAG GTGTCGGGACCAGTTGTCGTCGCAGATGGAATGGCAGGGGCTGCTATGTAT
genomic: CCACGTTCGAGGACTCGGAGAAGGAAAGCGAGTACGGTTACGTTCGCAAGgtacttttct ... catttgacagGTGTCGGGACCAGTTGTCGTCGCAGATGGAATGGCAGGGGCTGCTATGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaattgcgatgaatgggttattttcttgtgcacttaccatatatcatttgacagGTGTCGGGACCAGTTGTCGTCGCAGATGGAATGGCAGGGGCTGCTATGTATGAACTGGTCCGTGTTGGACATGACAACCTTATTGGAGAAATTATTCGGT
cacttac putative branch site (score: 2)
atatatcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtaatccgacaatatatggtttcttctttgatctaccaacatgttcaattgcgatgaatgggttattttcttgtgcacttaccatatatcatttgacagGTGTCGGGACCAGTTGTCGTCGCAGATGGAATGGCAGGGGCTGCTATGTATGAACTGGTCCGTGTTGGACATGACAACCTTATTGGAGAAATTATTCGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - -accaaca
- - - - - - - - - - - - - - - - - - - - - - - caattgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttacca