Sequence
atgc intronic sequence ATGC exonic sequence...acaattcagtgtatattatgctatagaatgtgcctttttcataactcatttccattaatttttattgtcattgaaaattattgtttgaattttctttcagAAATATGCAATGCAACAAGCTTTCAAGACTTTGATGGGCCAGATGGATTCACAAAATAACCAATTCAATACTACTACTTTTTCACCAGGATCGCCTTTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os04g35900.1 (Oryza sativa), 3'ss of exon 4
acaattcagtgtatatt-atgctatagaatgtgcctttttcat---aactcatttccattaatttttattgtca-ttgaaaattattgtttgaattttctttcagAAATATGCAATGCAACAAGCTTTCAAGACTTTGATGGGCCAGATGGATTCACAAAATAACCAATTCAATACTACTACTTTTTCACCAGGATCGCCTTTTC---
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---tctctttgtaggtttgatctgtataatgtcttgttggaacttaaaatcgtataactctcccttgcttgccagttttgacacattgct--aattctgatgcagAAATATGCAATGCAACAAGCATTCAAGTCAATGATGACCCAGGCACCGCCA-AACACTTTTGGCTCAAACTCGC--CTTTCCCATTTGCCATGCCACCACAGG
upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G05480.1 (Glycine max), 3'ss of exon 6
acaattcagtgtatattatg-cta--tagaatgtgcctttttcataactcatttccattaatttttattgtcattgaaaattattgtttgaattttctttcagAAATATGCAATGCAACAAGCTTTCAAGACTTTGATGGGCCAGATGGATTCACAAAATAACCAATTCAATACTACTACTTTTTCACCAGGATCGCCTTTTC
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-ttatttttcatggattttgactagtttcattgtagaattacaagagctaaccctgaacattttacatatt--ttaaacatttgtcttttgattttcttttagAAATATGCAATGCAACAAGCTTTCAAGACCATGATGGGCCAGATGAATTCACAAAATAACCAATTTGGCAATGCTGCCTTTTCTCCGGGATCTCCTTTTC
upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G31810.1 (Glycine max), 3'ss of exon 4
-acaattcagtgtatattatgctatagaatgtgcctttttcataactcatttccattaatttttattgtcattgaaaattattgtttgaattttctttcagAAATATGCAATGCAACAAGCTTTCAAGACTTTGATGGGCCAGATGGATTCACAAAATAACCAATTCAATACTACTACTTTTTCACCAGGATCGCCTTTTC
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ccttatttctcatggattttgactgggtttgctgtagaattacaagaactaaccctgaacatttacatattttaaacatttgtcttttgattt-cttttagAAATATGCAATGCAACAAGCTTTCAAGACCATGATGGGTCAGATGAATTCTCAAAATAACCAATTTGGCAATGCTGCCTTTTCTCCGGGATCACCTTTTCMapped 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|110699715|gb|EE076966.1|EE076966EST: TTCATGGGTGGCCTCAAACTTAAAG AAATATGCAATGCAACAAGCTTTCAAGACTTTGATGGGCCAGATGGATTCA
genomic: TTCATGGGTGGCCTCAAACTTAAAGgtgagtgtta ... tttctttcagAAATATGCAATGCAACAAGCTTTCAAGACTTTGATGGGCCAGATGGATTCA
EST:
gi|161714077|gb|FC064378.1|FC064378EST: TTCATGGGTGGCCTCAAACTTAAAG AAATATGCAATGCAACAAGCTTTCAAGACTTTGATGGGCCAGATGGATTCA
genomic: TTCATGGGTGGCCTCAAACTTAAAGgtgagtgtta ... tttctttcagAAATATGCAATGCAACAAGCTTTCAAGACTTTGATGGGCCAGATGGATTCA
EST:
gi|30136267|gb|CB921605.1|CB921605EST: CAAACTTAAAG AAATATGCAATGCAACAAGCTTTCAAGACTTTGATGGGCCAGATGGATTCA
genomic: CAAACTTAAAGgtgagtgtta ... tttctttcagAAATATGCAATGCAACAAGCTTTCAAGACTTTGATGGGCCAGATGGATTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttccattaatttttattgtcattgaaaattattgtttgaattttctttcagAAATATGCAATGCAACAAGCTTTCAAGACTTTGATGGGCCAGATGGATTCACAAAATAACCAATTCAATACTACTACTTTTTCACCAGGATCGCCTTTTC
cattaat putative branch site (score: 3)
ttttctttc putative PPT
attaatttttattgtc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acaattcagtgtatattatgctatagaatgtgcctttttcataactcatttccattaatttttattgtcattgaaaattattgtttgaattttctttcagAAATATGCAATGCAACAAGCTTTCAAGACTTTGATGGGCCAGATGGATTCACAAAATAACCAATTCAATACTACTACTTTTTCACCAGGATCGCCTTTTC
-caattca
- - - - - - - - - - - - -gaatgtg
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