Sequence
atgc intronic sequence ATGC exonic sequence...ccagcacaattattatcaattattttataacattacctttacatgctgttctctattggattaagggctgattatacctgattataaatttttcttgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCACTGTGTGTTGATATGACAGATAATGAGTTGGCATATTTAGAGTGCATCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g10560.1 (Oryza sativa), 3'ss of exon 3
ccagcacaattattatcaattattttataacattacctttacatgctgttctc--tattggattaagggctgattatacctgattataa-atttttcttgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCACTGTGTGTTGATATGACAGATAATGAGTTGGCATATTTAGAGTGCATCC
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-tgttgggagtatcatcaa--gtttcaaaatgttacttctgacagcagtctttggtatatgggaatcagtatattcactttctttgtgataattttcatgcagTTCCGGACGCATAAAGTTATATACAGGCGATATGCAGGACTGTTTTTCTCAATGTGTGTGGATATCACTGACAATGAGTTGGCATACTTGGAATGCATCC
upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AC195874.2_FGT002 (Zea mays), 3'ss of exon 3
ccagcacaattattatcaatt-attttata-acattacctttacatgctgttctctattggattaagggctgattatacctgattataaatttttct-tgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCACTGTGTGTTGATATGACAGATAATGAGTTGGCATATTTAGAGTGCATCC
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---aaatatttattattattggaccatgtggacctaaccactgagttctgaattcttctattactttgacttttggtactaatctgtaatttttcttatgcagTTTCGCACACACAAAGTTATCTACAGGAGATATGCTGGACTGTTTTTTTCAATATGTGTGGACATAACTGATAATGAATTGGCATACTTGGAATGCATTC
upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G37730.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------ccagcacaattattatcaattattttataacattacctttacatgctgttctctattggattaagggctgattatacctgatt----ataaatttttcttgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCACTGTGTGTTGATATGACAGATAATGAGTTGGCATATTTAGAGTGCATCC-
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tcagtgctctctccaccattttctccttcttcctttgctttcacgaagttgtaattgcattaattctgtcatgaatgttctatgaggttctgcttttgttgctcttaggttgtctaaattgttataacaattgatttgttggtaacttgtcttgcagtTTCGTACGCACAAGATAATATACAGGCGATATGCTGGGTTATTTTTCTCACTCTGTGTTGATATCACTGATAATGAGTTGGCGTATTTAGAGTGCATCCA
upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G40430.2 (Glycine max), 3'ss of exon 3
------------------------------------------------------ccagcacaattattatca--attattttataacattac-ctttacatgct-----gttctct-attggattaagggctgattatacctgattataaatttttcttgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCACTGTGTGTTGATATGACAGATAATGAGTTGGCATATTTAGAGTGCATCC
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gtcagtactctctccacgattttcaatttcttcctttgctttcgctgagttgtaattgcattatttctgacatgaatgttctatgaggttcttcttttgttgctcttaggttgtctcatttgctatacaattgattgccgtttgatagtaacttgtcttgcagTTTCGTACGCACAAGATAATATACAGGCGATATGCTGGGTTGTTTTTCTCAATCTGTGTTGATATCACTGATAATGAGTTGGCGTATTTAGAGTGCATCC
upper sequence: Vv18s0001g14240.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT1G47830.1 (Arabidopsis thaliana), 3'ss of exon 3
------ccagcacaattattatcaattattttataacattacctttacatgctgttctctat-tggattaagggctgattatacctgattataaatttttcttgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCACTGTGTGTTGATATGACAGATAATGAGTTGGCATATTTAGAGTGCATCC
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tgtgattgagaaacaataatatggaatgcgtttta----tgtgagtgggtgtcattgtgaatgttaatgtatgaatgatgaaactgttttgcaactatttt---cagTTTAGAACACACAAGGTGATATACAGGCGTTATGCTGGATTGTTTTTCTCTGTGTGCGTGGATATAACCGACAATGAGTTGGCTTACTTGGAGAGTATCCMapped 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|37188193|gb|CF607542.1|CF607542EST: TTCACCGATTGGTTGTCAACCGGGATCCCAAGTTCACTAACTTCGTTGAG TTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCA
genomic: TTCACCGATTGGTTGTCAACCGGGATCCCAAGTTCACTAACTTCGTTGAGgtattttctt ... tttcttgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCA
EST:
gi|71886235|gb|DT035290.1|DT035290EST: TTCACCGATTGGTTGTCAACCGGGATCCCAAGTTCACTAACTTCGTTGAG TTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCA
genomic: TTCACCGATTGGTTGTCAACCGGGATCCCAAGTTCACTAACTTCGTTGAGgtattttctt ... tttcttgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttctctattggattaagggctgattatacctgattataaatttttcttgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCACTGTGTGTTGATATGACAGATAATGAGTTGGCATATTTAGAGTGCATCC
acctgat putative branch site (score: 4)
tttttcttgc putative PPT
attatacctgattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccagcacaattattatcaattattttataacattacctttacatgctgttctctattggattaagggctgattatacctgattataaatttttcttgcagTTCCGTACACACAAGGTAATCTACAGGCGATATGCTGGATTATTTTTCTCACTGTGTGTTGATATGACAGATAATGAGTTGGCATATTTAGAGTGCATCC
-cagcaca
- - - - - - - - - - - - - - - cattacc
- - - - - - - - - - - - - - - - - - - ttacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgatt