Sequence
atgc intronic sequence ATGC exonic sequence...aaggttccttccattattgttaacttgaagacgcacatcatttttattatgcttttcctgcaatgaatccattaatcttctaacttattatactatgcagGTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTTTTTTGATCCTTCACGTGCTAAGGATTTTCTCTTCATTTCAGGAACCAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g02050.1 (Oryza sativa), 3'ss of exon 3
----aaggttccttccattattgttaacttgaagacgcacatcatttttatt----atgcttttcctgcaatgaatccattaatcttctaact-----tattatactatgcagGTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTTTTTTGATCCTTCACGTGCTAAGGATTTTCTCTTCATTTCAGGAACCAAG
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gtatttgatgcacagaaaaagcattagcatttaatgaattatcatttgttttgaggaaacatgtaataccagatttttgttctttccctaaaaataaatactatttgctccagGTAGCAGCATATGATACAGTGGCGAAGAAGATGGCGTTCTTTGATCCTTCACGGAGTAAAGATTTTCTGTTCATCTCAGGAACCAAG
upper sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g02050.2 (Oryza sativa), 3'ss of exon 3
----aaggttccttccattattgttaacttgaagacgcacatcatttttattatg----cttttcctgcaatgaatccattaatcttctaact-----tattatactatgcagGTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTTTTTTGATCCTTCACGTGCTAAGGATTTTCTCTTCATTTCAGGAACCAAG-------------
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gtatttgatgcacagaaaaagcattagcatttaatgaattatcatttgttttgaggaaacatgtaataccagatttttgttctttccctaaaaataaatactatttgctccagGTAGCAGCATATGATACAGTGGCGAAGAAGATGGCGTTCTTTGATCCTTCACGGAGTAAAGATTTTCTGTTCATCTCAGGAACCAAGGTACAGATAAATT
upper sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G158147_T01 (Zea mays), 3'ss of exon 3
-----aaggttccttccattattgttaacttgaagacgcacatcatttttattatgcttttcctgcaatgaatccattaatcttctaacttattatactat-gcagGTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTTTTTTGATCCTTCACGTGCTAAGGATTTTCTCTTCATTTCAGGAACCAAG
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tgtgcactaatgattcaatt--tgtttgttttaccaaaaacttg--tttgatttttcatctcctgttatc--ttgaatgctctcttgttttgctatcctcttacagGTAGCAGCTTATGATACAGTAGCAAAGGAGATGGCCTTTTTTGATCCTTCACGCAGTCAAGATTTTCTGTTCATCTCTGGAACCAAG
upper sequence: Vv18s0001g14010.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G19920.1 (Arabidopsis thaliana), 3'ss of exon 3
aaggttccttccattattgttaacttgaagacgcacatcatttttattatgcttttcctgcaatgaatccattaatcttctaac-------ttattatactatgcagGTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTTTTTTGATCCTTCACGTGCTAAGGATTTTCTCTTCATTTCAGGAACCAAG
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---gtaacacaaatcgattctgactgcaaaac-caaagtttcttgattatttgattatcggaatatgctgcttcaattcccaatcatgtgttctttgtatctttcagGTTGCAGCTTACGATACAATCGAGAAGAAGATGGCGTTTTTCGATCCTTCTCGTGCAAAAGAGTTTCTTTTCATTTCTGGAACAAAGMapped 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|34542781|gb|CF511013.1|CF511013EST: TGTTAAGCATGGCTCCTGGCTTGGAGAAGCTAAATATTCTGCCATTCAGG GTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTTTTTTGATCCTTCA
genomic: TGTTAAGCATGGCTCCTGGCTTGGAGAAGCTAAATATTCTGCCATTCAGGgtaggttttt ... tactatgcagGTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTTTTTTGATCCTTCA
EST:
gi|26264548|gb|CA815611.1|CA815611EST: TGTTAAGCATGGCTCCTGGCTTGGAGAAGCTAAATATTCTGCCATTCAGG GTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTCTTTTGATCCTTCA
genomic: TGTTAAGCATGGCTCCTGGCTTGGAGAAGCTAAATATTCTGCCATTCAGGgtaggttttt ... tactatgcagGTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTTTTTTGATCCTTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatgcttttcctgcaatgaatccattaatcttctaacttattatactatgcagGTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTTTTTTGATCCTTCACGTGCTAAGGATTTTCTCTTCATTTCAGGAACCAAG
ttctaac putative branch site (score: 1)
attaatcttctaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaggttccttccattattgttaacttgaagacgcacatcatttttattatgcttttcctgcaatgaatccattaatcttctaacttattatactatgcagGTTGCAGCATATGACACAGTGGGAAAGAAGATGGCCTTTTTTGATCCTTCACGTGCTAAGGATTTTCTCTTCATTTCAGGAACCAAG
- - - ccttcca
- - - - - - - - - - - - - - -gacgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatcca