Sequence
atgc intronic sequence ATGC exonic sequencegtcacattcatgccctatttgcattagtaattcttcttaatgttgtaaagtgttaaaaaaatctgttttctattgtgtggctcatttttctagtgttctatttatttatactgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTTAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCA
Basic information
species | Glycine max |
transcript | GLYMA13G42070.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g34100.1 (Oryza sativa), 3'ss of exon 4
gtcacattcatgccctatttgcattagtaattcttcttaatgttgtaaagtgttaaaaaaatctgttttctattgtgtggctcatttttctagtgttctatttatttatactgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTTAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCA
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-ttatatt---gcgatttttgcatc-----ttatgtttatttacaagatatgtcaatactatctttttttttaaaaaaaaatca-----ccaatttcccttctacttatatt------agGTCATGTGTGCTACCACTTCCCTGGATCTGGAGCAATATTTACAGGGGACACATTGTTTAGTTTGTCATGTGGAAAGCTTTTTGAAGGGACTCCACAACA
upper sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 4
lower sequence: AT2G31350.2 (Arabidopsis thaliana), 3'ss of exon 4
gtcacattcatgccctatttgcattagtaattcttcttaatgttgtaaagtgttaaaaaaatctgttttctattgtgtggctcatttttctagtgttctatttatttatactgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTTAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCA
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------ttttgacggtttctgcgaaaaccatccc-------gttatatacctcttaagcgttgt-tgtcccatgttttagtctttgtctcttatcttct---taattatact---tgcagGCCATATCAGCTTATACTTTCCAGGATCACGAGCGATCTTCACCGGGGACACGATGTTTAGCTTATCATGTGGTAAACTCTTTGAAGGCACTCCTAAGCA
upper sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G06130.2 (Arabidopsis thaliana), 3'ss of exon 4
gtcacattcatgccctatttgcattagtaattcttcttaatgttgtaaagtgttaaaaaaatctgttttctattgtgtggctcatttttctagtgttctatttatttatactgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTTAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCA
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-----aactattgaagatttgc--tggtttcggttcctca-aacataaactatgcacagtatatgcttaa-gccttgtc-cccatttt---aatgtcccatttt------ctgt-tgtagGCCATATTAGTTTCTACTTTCCAGGGGCACGAGCAATTTTCACCGGGGACACCTTGTTTAGCTTATCATGTGGTAAACTCTTCGAAGGTACTCCAGAGCA
upper sequence: GLYMA13G42070.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0102g01180.t01 (Vitis vinifera), 3'ss of exon 6
gtcacattcatgccctatttgcattagtaattcttcttaatgttgtaaagtgttaaaaaaatctgttttctattgtgtggctcatttttctagtgttctatttatttatactgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTTAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCA
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-ttatatttggcttctagattcac--atagttccccctttttcttttctttattaataa-----------tttaacctaatttaattttgtg------tattgattttaattgcaagcagGCCACATTAGCTTCTACTTTCCGGGATCAGGGGCAATTTTTACAGGGGACACTTTGTTCAGTCTATCATGTGGCAAACTTTTCGAAGGAACTCCTGAACAMapped 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|254314674|gb|GR829667.1|GR829667EST: GTTTGCTGGCCATGAGGTGCGTGTAATGGACACGCCTGGTCATACCCGAG GCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACA
genomic: GTTTGCTGGCCATGAGGTGCGTGTAATGGACACGCCTGGTCATACCCGAGgtcacattca ... ctgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACA
EST:
gi|31309192|gb|CD394395.1|CD394395EST: GTGTAATGGACACGCCTGGTCATACCCGAG GCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACA
genomic: GTGTAATGGACACGCCTGGTCATACCCGAGgtcacattca ... ctgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttctattgtgtggctcatttttctagtgttctatttatttatactgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTTAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCA
atttttctagtgttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcacattcatgccctatttgcattagtaattcttcttaatgttgtaaagtgttaaaaaaatctgttttctattgtgtggctcatttttctagtgttctatttatttatactgtatgcagGCCATATAAGCTTCTATTTTCCTGGATCTGGGGCAATTTTTACTGGAGACACTTTGTTTAGCTTATCATGTGGCAAGCTCTTTGAAGGAACCCCACAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA