Sequence
atgc intronic sequence ATGC exonic sequencegtaagatttccatcctttccttttgtaggcatgttgtgaaaatatatggtttattaatatggattagttgtgtttatatccttaaaattcagtatccttaacattccctacttgcttgcatgaacatgcctcagGTGTATGCATCTGATAGTATTTCCCCGAGCATCAAGCCACCTCCAATTAATGATGGAACCCCAAATGAGAGCGTTGAAGATGTGTTTGTTCGTGTGACAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g08200.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g47190.1 (Oryza sativa), 3'ss of exon 2
gtaagatttccatcctttccttttgtaggcatgttgtgaaaatatatggtttattaatatggattagttgtgtttatatccttaaaattcagtatccttaacattccctacttgcttgcatgaacatgcctcagGTGTATGCATCTGATAGTATTTCCCCGAGCATCAAGCCACCTCCAATTAATGATGGAACCCCAAATGAGAGCGTTGAAGATGTGTTTGTTCGTGTGACAC
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----------------------------tctttttctgaagcttcttcggtt-----tatggatcagccatttttttgcttggtaaattccatcctgttctcattgaat-ttccctttcttgctatggatttagGTGTATGCATCAGACAGTATTTCGCCAGACATCAAGCCACCTCCTATTAGTGATGGTACACCAAATGAGAGTGTTGCAGATGTATTTGTTCGGGTAACGC
upper sequence: Vv17s0000g08200.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G098973_T01 (Zea mays), 3'ss of exon 2
gtaagatttccatcctttccttttgtaggcatgttgtgaaaatatatggtttattaatatggattagttgtgtttatatccttaaaattcagtatccttaacattccctacttgcttgcatgaacatgcctcagGTGTATGCATCTGATAGTATTTCCCCGAGCATCAAGCCACCTCCAATTAATGATGGAACCCCAAATGAGAGCGTTGAAGATGTGTTTGTTCGTGTGACAC
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---------------cttcaattgagctgcatgctctaacattagattgttt-ttgcaacaaatttactcctattgtgcc--tgaactatgcttttcttggcat---------gatggc-------tgcattagGTGTACGCGTCAGATAATATTTCTCCAGACTTGAAGCCTCCTCCTATCAGGGATGGTACTCCAAATGAGAGCGTTGCAGATGTATTTGTGCGGGTGACAC
upper sequence: Vv17s0000g08200.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G02120.1 (Glycine max), 3'ss of exon 2
gtaagatttccatcctttccttttgtaggcatgttgtgaaaatatatggtttattaatatggattagttgtgtttatatccttaaaattcagtatccttaacattccctacttgcttgcatgaaca--tgcctcagGTGTATGCATCTGATAGTATTTCCCCGAGCATCAAGCCACCTCCAATTAATGATGGAACCCCAAATGAGAGCGTTGAAGATGTGTTTGTTCGTGTGACAC
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----------------------------------tttacaaatttcctacatgcttgttttgatgagctaaagtgggatttgtgca--ttgatgttaagaacgtatctgagtgtggggaattttcaaatgctccagGTGTATGCATCAGATGGTATATCTCCGAACATCAAGCCTCCTCCCATTAATGACGGAACTCCGAATGAGAGTGTTGCAGATGTTTTTGTTCGTGTGACACMapped 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|22009715|gb|BQ794749.1|BQ794749EST: CCCGTGGACTGGGAGCTTTTGAAGGCAAGAACTTGGAATCTGTTTCTGAA GTGTATGCATCTGATAGTATTTCCCCAAGCATCAAGCCACCTCCAATTAAT
genomic: CCCGTGGACTGGGAGCTTTTGAAGGCAAGAACTTGGAATCTGTTTCTGAAgtaagatttc ... catgcctcagGTGTATGCATCTGATAGTATTTCCCCGAGCATCAAGCCACCTCCAATTAAT
EST:
gi|22008705|gb|BQ793739.1|BQ793739EST: CCCGTGGACTGGGAGCTTTTGAAGGCAAGAACTTGGAATCTGTTTCTGAA GTGTATGCATCTGATAGTATTTCCCCAAGCATCAAGCCACCTCCAATTAAT
genomic: CCCGTGGACTGGGAGCTTTTGAAGGCAAGAACTTGGAATCTGTTTCTGAAgtaagatttc ... catgcctcagGTGTATGCATCTGATAGTATTTCCCCGAGCATCAAGCCACCTCCAATTAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttaaaattcagtatccttaacattccctacttgcttgcatgaacatgcctcagGTGTATGCATCTGATAGTATTTCCCCGAGCATCAAGCCACCTCCAATTAATGATGGAACCCCAAATGAGAGCGTTGAAGATGTGTTTGTTCGTGTGACAC
ccttaac putative branch site (score: 3)
ttaacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatttccatcctttccttttgtaggcatgttgtgaaaatatatggtttattaatatggattagttgtgtttatatccttaaaattcagtatccttaacattccctacttgcttgcatgaacatgcctcagGTGTATGCATCTGATAGTATTTCCCCGAGCATCAAGCCACCTCCAATTAATGATGGAACCCCAAATGAGAGCGTTGAAGATGTGTTTGTTCGTGTGACAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG