Sequence
atgc intronic sequence ATGC exonic sequence...cataccaaatactacatgcatttgtctctgagcattcatttgtattgcatctttcaattctattgtctaacattctaactattcatgctgatctatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATG
Basic information
species | Glycine max |
transcript | GLYMA03G40980.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g41520.1 (Oryza sativa), 3'ss of exon 4
cataccaaatactacatgcatttgtctctgagcattcatttgtattgcatctttca-attctattgtctaacattctaactattcatgctgatcta--tccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATG
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--tttcagatttagaacgttttaacaccttatgatat-ctcatcatatataatccacagcctgctgattatttgtaaacgtcgccttcctaactttgctgcagTGGATGGTTGATGAGAAAGAACTTAGGGTCATTCACTACACACTTGGGCCTCTTAAGCCCTGGGACTGGTGGACTGCTTGGCTTGTTAAACCTGTGGCAG
upper sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G18480.1 (Arabidopsis thaliana), 3'ss of exon 3
-cataccaaatactacatgcatttgtctctgagcattcatttgtattgc-atctttcaattctattgtctaacattctaactattcatgctgatctatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATG
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acgtagtggttaatttggg-attggttttgattggtttaaaagtataactgtctttttcttcagctgtttgaatctttgtgttttctcatt-atttctgcagTGGATGGTTGATGACAGTAAACTTCACGTCATTCACTACACTCTAGGCCCTCTTAAGCCTTGGGACTGGTGGACAGCATGGCTCGTGAAACCTGTTGATG
upper sequence: GLYMA03G40980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0036g00430.t01 (Vitis vinifera), 3'ss of exon 4
cataccaaatactacatgcatttg---tctctgagcattcatttgtattgcatctttcaattctattgtctaacattctaa-ctattcatgc-tgatctatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATG
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--caagaaatccttagtaggactgaggcctgcatgcttctgattgttttaaatctgccaattggaaaa---aaaattctcatctgtttatgtgtggtaaatgcagTGGATGGTAGATGAAGAAAAACTCCGTGTTATCCACTACACACTTGGCCCCCTTAAACCATGGGATTGGTGGACGTCTTGGCTTCTAAAACCTGTTGATGMapped 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|208255782|gb|GE052761.1|GE052761EST: CTTGCTAACAAG TGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCC
genomic: CTTGCTAACAAGgtactataat ... atctatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCC
EST:
gi|14012150|gb|BG727072.1|BG727072EST: TATCAACACTGTATAACGCTGATGTTGGTCTTTACATGCTTGCTAACAAG TGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCC
genomic: TATCAACACTGTATAACGCTGATGTTGGTCTTTACATGCTTGCTAACAAGgtactataat ... atctatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatctttcaattctattgtctaacattctaactattcatgctgatctatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATG
tctatcc CT-rich tract
aattctatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cataccaaatactacatgcatttgtctctgagcattcatttgtattgcatctttcaattctattgtctaacattctaactattcatgctgatctatccagTGGATGGTAGATGAGAATGAACTCCGTGTGATTCACTATACACTGGGCCCCCTTAAGCCTTGGGACTGGTGGACGTCTTGGCTTTTGAAACCTGTTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
catacca
- - - - - - -acatgca
- - - - - - - - - - - -gtctctg
- - - - - - - - - - - - - - - -gcattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgct