Sequence
atgc intronic sequence ATGC exonic sequence...tgcacctgacattgccaaagctcctgcattttagtgtttgtgcttctttggtgggatgaaattttatatcctgattttccctgttctttctttcgtgtagGATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGAAGTACATGTAAATTTCACCATCCTCAACCATCTAGTATGATGGTTTCAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 4
-------tgcacctgacattgccaaa-gctcctgcattttagtgtttgtgcttctttggtgggatgaaattttat----atcctgattttccctgttc---tttctttcgtgtagGATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGAAGTACATGTAAATTTCACCATCCTCAACCATCTAGTATGATGGTTTCAT
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gtttgttctaaatttccattatcttttactattacttgttggacttaaggatagttcattattctgcaacttctctgcaatatttgttttagttacctaaattttattaccacagAATGAGAAGGAATGCGCTTATTATTTAAGAACCGGACAGTGCAAATTTGGGAGCACATGTAAGTTTCATCATCCACAGCCATCTAATACGATGGTTGCTG
upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g68860.1 (Oryza sativa), 3'ss of exon 4
tgcacctgacattgccaaagctcctgcattttag-tgtttgtgcttctttggtgggatgaaattttatatcctgattttccctgttctttctttcgtgtagGATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGAAGTACATGTAAATTTCACCATCCTCAACCATCTAGTATGATGGTTTCAT
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---gtttgtagtt--tattgctgcagcacatcatctgcccttcctttttatagtttcttctctttgatgtactgaagtgaagtctgtttgcttc--tgtagAGTGAAAAGGAGTGTGCATATTACTTAAAAACAGGACAGTGTAAATATGGGAATACATGTAAATTTCACCATCCAGAACTTTTCAATGCTATGGCTTCTT
upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G100794_T01 (Zea mays), 3'ss of exon 4
-------------tgcacctgacattgccaaagctcctgcattttagtgttt---gtgcttctttggtgggatgaaattttatatcctgattttccctgttc-------tttctttcgtgtagGATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGAAGTACATGTAAATTTCACCATCCTCAACCATCTAGTATGATGGTTTCAT
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gtttgttctgaatttctattacaattcataatgtttcacgatatgaatgcatagcatggtgccacatttttgtgcaacttttttgcaagatttgcgccgtttacttgaattttattactgcagAATGAAAAGGAATGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGAAGCACATGTAAGTTTCACCATCCACAACCATCCACTATGATGGTTGCCG
upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G146514_T03 (Zea mays), 3'ss of exon 4
-------------------tgcacctgacattgccaaagctcctgcattttagtgtttgtgcttctttggtgggatgaaattttata----tcctgattttccctgttctttctttcgtgtagGATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGAAGTACATGTAAATTTCACCATCCTCAACCATCTAGTATGATGGTTTCAT
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gtttgttctgaatttctattacaattcacaatgtttcatgatatgaatgcatactattgtgccgcctttctatgcaacatttttgcaagatttgtgttgtttacttgaattttattactgcagAATGAAAAAGAGTGTGCTTATTATTTAAGAACAGGGCAGTGCAAGTTTGGAAGCACATGTAAGTTTCACCATTCACAACCATCCACCATGATGGTTGCTG
upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 4
tgcacctgacattgcca---aagctcctgcattttagtgtttgtgcttctttggtgggatgaa--attttatatcctgattttccctgttctttctttcgtgtagGATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGAAGTACATGTAAATTTCACCATCCTCAACCATCTAGTATGATGGTTTCAT
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---agataatttttctatttaatatctgacacctgattgttt-tgtttgattgctgatattaataatctaattcaatatttttttctgtttctt-tttgatacagAATGAGCCTGAATGTGCTTATTATTTAAGAACTGGACAATGTAAATTTGGGAACACTTGCAAATTTCACCATCCTCAACCAAACAATATGGTGCTTTCCA
upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 4
tgcacctgacattgccaaagctcctgcattttagtgtttgtgcttctttggtgggatgaa-attttatatcctgattttccctgttctttctttcgtgtagGATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGAAGTACATGTAAATTTCACCATCCTCAACCATCTAGTATGATGGTTTC-AT
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tgataattcttctatttaatatctgacacctgattgttt-tgtgggattactgatattattaatctaattctatattttctttgtttctt-tttgatacagaATGAACCAGAATGTGGTTATTATTTAAGAACTGGACAATGTAAATTTGGGAACACTTGCAAATTTCACCATCCTCAACCAAACAATATGGTGCTTTCCAT
upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G31370.2 (Glycine max), 3'ss of exon 3
--tgca-cctgacattgccaaagctcctgcattttagtgtttgtgcttctttggtgggatgaaattttatatcctgattttccctgttctttctttcgtgtagGATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGAAGTACATGTAAATTTCACCATCCTCAACCATCTAGTATGATGGTTTCAT
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tctgaatcctgaacctttcatagatattttgctt-gctttctggttgatattaatgttctcgtaacttacaatgt-atttccgatgtttcctgattc-tgcagAATGAGCCTGAATGCACTTATTATTTGAGAACCGGACAATGCAAATTTGGGAACACTTGCAAATTCCACCATCCTCAACCAAGTAATATGATGCTCTCAT
upper sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 4
tgcacctgacattgccaaagctcctgcattttagtgtttgtgcttctttggtgggatgaaa--ttttatatcctgat-tttccctgttctttctt--tcgtgtagGATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGAAGTACATGTAAATTTCACCATCCTCAACCATCTAGTATGATGGTTTCAT
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--tatttga--tccctgaacctttcgtagac-attttgcttgctttctgattgaaattaatgttctcataacttaatatatttccgatggttcctgattctgcagAATGAGCCTGAATGCACTTATTATTTGAGAACAGGACAATGCAAATTTGGGAACACTTGCAAATTCCACCATCCTCAACCAAGTAATATGATGCTCTCATMapped 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|110384276|gb|EC948703.1|EC948703EST: GAATTGCTGGAAGAGTTTCTTTAAATATTTTAGGCTATCCACTGCGGCCG GATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGA
genomic: GAATTGCTGGAAGAGTTTCTTTAAATATTTTAGGCTATCCACTGCGGCCGgttcgatttt ... tttcgtgtagGATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttggtgggatgaaattttatatcctgattttccctgttctttctttcgtgtagGATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGAAGTACATGTAAATTTCACCATCCTCAACCATCTAGTATGATGGTTTCAT
tcctgat putative branch site (score: 3)
tatcctgattttccct CT-rich tract
atgaaattttatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcacctgacattgccaaagctcctgcattttagtgtttgtgcttctttggtgggatgaaattttatatcctgattttccctgttctttctttcgtgtagGATGAGATTGACTGTGCTTATTATTTAAGAACTGGACAGTGCAAGTTTGGAAGTACATGTAAATTTCACCATCCTCAACCATCTAGTATGATGGTTTCAT
- cacctga
- - - - - - - ccaaagc
- - - - - - - - - - -tcctgca
- - - - - - - - - - - - - - - - - - tttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - tggtggg