Sequence
atgc intronic sequence ATGC exonic sequence...aaagttatgggaacttggcaaacatgaggatttctgcaatctttaacttcattaaacttgtgtacttgtgatctaatgcgtcttgatgctctaaaagcagGAGTTACAGTCCCCGCGGGCGATCCCCAAGACGCCGCAGTTTGTCTCCTCGTGGGCGCAGCTATAGCAGGTCACCAGGATATCGTGGACGTGAGGAATTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G151923_T01 (Zea mays), 3'ss of exon 4
-aaagttatgggaacttggcaaaca----tgaggatttctgcaatctttaacttcattaaacttgtgtacttgtgatctaatgcgtcttgatgctctaaaagcagGAGTTACAGTCCCCGCGGGCGATCCCCAAGACGCCGCAGTTTGTCTC---CTCGTGGGCGCAGCTATAGCAGGTCACCAGGATATC---GTGGACGTGAGGAATTG
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ctattcaatctgtacttgggaaatactcttagcaaattgcataattcatgttatgaacaaaggacaatgaatctgatcgaattcatat-----ctttacaaacagGAGTTACAGTCCTGCAGCACGCTCTCCAAGGCGTCGTAGCGTCTCACCAGCTCGTGGACGCAGCTATAGCAGGTCACCACAGCACAAGGGTGCACGTGAA------
upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G29080.1 (Glycine max), 3'ss of exon 4
aaagttatggga--acttggcaaacatgaggatttctgcaatctttaacttcattaaacttgtgtacttgtgatctaatgcgtcttgatgctctaaaagcagGAGTTACAGTCCCCGCGGGCGATCCCCAAGACGCCGCAGTTTGTCTCCTCGTGGGCGCAGCTATAGCAGGTCACCAGGATATCGTGGACGTGAGGAATTG
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cttgttattaaatggttgggtgtgtttgtatgattttgtgataat-aattttatcttgtaaatctttatgttcttttct-cacctttcttttgtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCGCCGTAGTTTGTCACCTCGTGGACGTAGCTACAGCAGGTCACCTCCTTATCGTGGGCGTGAGGAGGTC
upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G29080.2 (Glycine max), 3'ss of exon 4
aaagttatgggaacttggcaaacatgaggatttctgcaatctttaacttcattaaacttgtgtacttgtgatctaatgcgtcttgatgctctaaaagcagGAGTTACAGTCCCCGCGGGCGATCCCCAAGACGCCGCAGTTTGTCTCCTCGTGGGCGCAGCTATAGCAGGTCACCAGGATATCGTGGACGTGAGGAATTG---------
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-------aaatggttgggtgtgtttgtatgattttgtgataat-aattttatcttgtaaatctttatgttcttttct-cacctttcttttgtatgactaggagttacagTCCTCGTGGGCGGTCCCCTAGGCGCCGTAGTTTGTCACCTCGTGGACGTAGCTACAGCAGGTCACCTCCTTATCGTGGGCGTGAGGAGGTCCCATATGCT
upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G17930.3 (Glycine max), 3'ss of exon 4
-------aaagttatgggaacttggcaaacatgaggatttctgcaatctttaacttcattaaacttgtgtacttgtgatctaatgcgtcttgatgctctaaaagcagGAGTTACAGTCCCCGCGGGCGATCCCCAAGACGCCGCAGTTTGTCTCCTCGTGGGCGCAGCTATAGCAGGTCACCAGGATATCGTGGACGTGAGGAATTG
| ||| || | ||| || | || ||| || | | || || ||| | | | | ||| | |||| | || | |||||||||||||| || ||||| ||||| || | |||||||||||| |||||||| || ||||| |||||||| || |||||||| |||||||| |
ctatcttgtaattaaaggg-ttgggcgtgtttgtaggttgaaataatagtttatcttataaatctt-tatgttcttt-tctcacctttctta----tgtatgactagGAGTTACAGTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCGTGGACGTAGCTACAGCAGGTCTCCTCCTTATCGTGGGCGTGAGGAGGTT
upper sequence: Vv04s0069g00800.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA14G17930.2 (Glycine max), 3'ss of exon 4
aaagttatgggaacttggcaaacatgaggatttctgcaatctttaacttcattaaacttgtgtacttgtgatctaatgcgtcttgatgctctaaaagcagGAGTTACAGTCCCCGCGGGCGATCCCCAAGACGCCGCAGTTTGTCTCCTCGTGGGCGCAGCTATAGCAGGTCACCAGGATATCGTGGACGTGAGGAATTG---------
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--aattaaaggg-ttgggcgtgtttgtaggttgaaataatagtttatcttataaatctt-tatgttcttt-tctcacctttctta----tgtatgactaggagttacagTCCTCGTGGGCGGTCCCCTAGGCACCGCAGTTTGTCACCTCGTGGACGTAGCTACAGCAGGTCTCCTCCTTATCGTGGGCGTGAGGAGGTTCCTTATGCTMapped 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|85153366|gb|DW588056.1|DW588056EST: CAGTCGCAGCCCTAGGTACCGCAGGAGCCCAAGTTATGGTCGTAG GAGTTACAGTCCCCGCGGGCGATCCCCAAGACGCCGCAGTTTGTCTCCTCG
genomic: CAGTCGCAGCCCTAGGTACCGCAGGAGCCCAAGTTATGGTCGTAGgtgagatggt ... ctaaaagcagGAGTTACAGTCCCCGCGGGCGATCCCCAAGACGCCGCAGTTTGTCTCCTCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttcattaaacttgtgtacttgtgatctaatgcgtcttgatgctctaaaagcagGAGTTACAGTCCCCGCGGGCGATCCCCAAGACGCCGCAGTTTGTCTCCTCGTGGGCGCAGCTATAGCAGGTCACCAGGATATCGTGGACGTGAGGAATTG
ctctaaa putative branch site (score: 3)
attaaactt 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
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aaagttatgggaacttggcaaacatgaggatttctgcaatctttaacttcattaaacttgtgtacttgtgatctaatgcgtcttgatgctctaaaagcagGAGTTACAGTCCCCGCGGGCGATCCCCAAGACGCCGCAGTTTGTCTCCTCGTGGGCGCAGCTATAGCAGGTCACCAGGATATCGTGGACGTGAGGAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - ttatggg
- - - - - - - - -gcaaaca
- - - - - - - - - - - - - - - - -ctgcaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct