Sequence
atgc intronic sequence ATGC exonic sequence...ataacatcagcattttattaaattctttggcattccagattaacttcttcagtagtaattatcaaataaccaaggttgtcaattgtttttgttgagtcagGTTAGTCATCACCCTATGATTGTTGCATGTCACTGTGAGGGTACGGGATGGAAATTTTGGGCAGATAGCAATTTAAAGAGCAAATTTTGGGGTCGGTCTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g49770.2 (Oryza sativa), 3'ss of exon 5
ataacatcagcattttattaaattctttggcattccagattaacttcttcag-tagtaattatcaaataaccaaggttgtcaattgtttttgttgagt---------cagGTTAGTCATCACCCTATGATTGTTGCATGTCACTGTGAGGGTACGGGATGGAAATTTTGGGCAGATAGCAATTTAAAGAGCAAATTTTGGGGTCGGTCTA
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----------tatatgcttgaatatttttcccctatagattattgtcttctgctagttctatttggatttgcattttggttgattaagactcttcaatatgacttgccagGTTAGTCACCATCCTATGGTGGTTGCATGCCATTGTGAGGGAACTGGGTGGCGGTTTTGGGCAGATAGCAACCTAAAAAGCAAGTTCTGGGGTCGCTCCA
upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G147332_T01 (Zea mays), 3'ss of exon 5
------------ataacatcagcattttattaaattctttggcattccagattaacttcttcagtagtaattatcaaataaccaaggttgtcaattgtttttgttgagtcagGTTAGTCATCACCCTATGATTGTTGCATGTCACTGTGAGGGTACGGGATGGAAATTTTGGGCAGATAGCAATTTAAAGAGCAAATTTTGGGGTCGGTCTA
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acccaaaccattgctacttgagcgtactacatgact-tttgcaatatcagatctagtttatttgcatta-ttgttgatgaa--aaaatt-tcaaccactt-------gccagGTTAGTCATCACCCTATGGTTGTTGCTTGCCACTGTGAGGGAACTGGCTGGAGGTTTTGGGCTGATAGCAACCTAAAGAGTAAATTCTGGGGTCGTTCCA
upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G157172_T01 (Zea mays), 3'ss of exon 6
------------ataacatcagcattttattaaattctttggcattccagattaacttcttcagtagtaattatcaaataaccaaggttgtcaattgtttttgttgagtcagGTTAGTCATCACCCTATGATTGTTGCATGTCACTGTGAGGGTACGGGATGGAAATTTTGGGCAGATAGCAATTTAAAGAGCAAATTTTGGGGTCGGTCTA
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tcacaaatcatagctacttgagcgtacaacatgact-tttgcaatataggatctaatttctttgcatcatttttta--tga--aaaatcttcaaccactt-------gccagGTTAGTCATCACCCTATGGTTATTGCATGCCACTGTGTGGGAACTGGCTGGAGGTTTTGGGCTGATAGCAACCTGAAGAGTAAATTCTGGGGTCGTTCCA
upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------------------------------------------ataacatcagca--ttttattaaat--tctttggcattc-cagattaacttcttcagtagtaatta---tcaaataacc-aaggttgtcaattgtttttgttgag---tcagGTTAGTCATCACCCTATGATTGTTGCATGTCACTGTGAGGGTACGGGATGGAAATTTTGGGCAGATAGCAATTTAAAGAGCAAATTTTGGGGTCGGTCTA
| | ||| | | | ||| || | || ||| | || | |||| || || | |||| | | | ||| | || || || || | |||||| || ||||| || |||||||| ||||||||||| ||||| | || ||||||||||||| || ||||| || || ||||| |||||||| || ||||
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S67_260V6.1 (Physcomitrella patens), 3'ss of exon 5
ataacatcagcattttattaaattctttggcattccagattaacttcttcagtagtaattatcaaataaccaaggttgtcaattgtttt-tgttgagt--cagGTTAGTCATCACCCTATGATTGTTGCATGTCACTGTGAGGGTACGGGATGGAAATTTTGGGCAGATAGCAATTTAAAGAGCAAATTTTGGGGTCGGTCTA
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--ggagatattaatttgc-aacctctttgtcatatctttcgagctttagattaagtaaaagttaatcatcttgcatcttctatctccctacgttgctttgcagGTGAGTCATCATCCAATGATTGTGGCATGTCATTGCGAGGGCAGAGGCTGGAAATTCTGGGGTGACAGCAATTTGAAAAGCAAGTTTTGGGGTCGTTCAA
upper sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S427_40V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------ataacatcagcattttattaaat-tctttggcattccagattaacttcttcagtagtaattatcaaat--aaccaaggttgtc---aattgtttttgttgagtc--agGTTAGTCATCACCCTATGATTGTTGCATGTCACTGTGAGGGTACGGGATGGAAATTTTGGGCAGATAGCAATTTAAAGAGCAAATTTTGGGGTCGGTCTA
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gtttgacgcgattgtcattttctattgtttgacaatctcttaggagtctgatggaattgccacatttgttcgcgccgagatgtttctggtacttgtgcttcatctctaaggaattgtaggttggactgaactataattatctgaaatcctctgttttgcggcgcagGTGAGCCATCACCCAATGATCGTGGCATGTCACTGCGAGGGTCGAGGATGGAAATTCTGGGGAGACAGCAACTTGAAAAGCAAGTTTTGGGGTCGTTCTAMapped 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|161717040|gb|FC065900.1|FC065900EST: CCTATGAGGCTGATTATCCAGATAAAGGCCTCCGTTTTTTCTCAGAGAAG GTTAGTCATCACCCTATGATTGTTGCATGTCACTGTGAGGGTACGGGATGG
genomic: CCTATGAGGCTGATTATCCAGATAAAGGCCTCCGTTTTTTCTCAGAGAAGgtatgttaaa ... gttgagtcagGTTAGTCATCACCCTATGATTGTTGCATGTCACTGTGAGGGTACGGGATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttcagtagtaattatcaaataaccaaggttgtcaattgtttttgttgagtcagGTTAGTCATCACCCTATGATTGTTGCATGTCACTGTGAGGGTACGGGATGGAAATTTTGGGCAGATAGCAATTTAAAGAGCAAATTTTGGGGTCGGTCTA
aaataac putative branch site (score: 2)
tttttgtt putative PPT
tagtaattatcaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ataacatcagcattttattaaattctttggcattccagattaacttcttcagtagtaattatcaaataaccaaggttgtcaattgtttttgttgagtcagGTTAGTCATCACCCTATGATTGTTGCATGTCACTGTGAGGGTACGGGATGGAAATTTTGGGCAGATAGCAATTTAAAGAGCAAATTTTGGGGTCGGTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - catcagc
- - - - - - - - - - - - - - -gcattcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaccaa