Sequence
atgc intronic sequence ATGC exonic sequence...ttctttaatttgcccttctttttgtgaatcaagggatgtaactaaagtggtcttttaaatttttagttttcctacataacattagctaaatttctctcagGAATTTAATAAGCATGACAAAGAACCAGGCAAGTACATCAAGCATTGGAGAGGTATTAAACCAAAGACGGGGGCACCATATTCATGTGATATTGGCTATG
Basic information
species | Glycine max |
transcript | GLYMA08G13780.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------ttctttaatttgcccttctttttgtgaatcaaggga-tgta-actaaagtggtcttttaaatttttagttttcctacataacattagctaaatttctctcagGAATTTAATAAGCATGACAAAGAACCAGGCAAGTACATCAAGCATTGGAGAGGTATTAAACCAAAGACGGGGGCACCATATTCATGTGATATTGGCTATG
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gtaatccttagtggtgaatattcaagtcagataatattaatatatactcttctgaaaatttattactggcctgtatgctgaaatcgcttgaaaagaatataggaatattg-ataaagaacattcatatggttgcagGAGTTTAATAAACATGACAAAGAACCAGCAAAGTATATTAAACAATGGAAAGGTGTAAAGCCAAAGACTGGTGCACCATACACTTGCGACGTGGGATATG
upper sequence: GLYMA08G13780.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 4
-----ttctttaatttgcccttct--ttttgtgaatcaagggatgtaactaaagtggtct------------------ttta-------aatttttagttt---tcctacataacattagctaaatttctct-------cagGAATTTAATAAGCATGACAAAGAACCAGGCAAGTACATCAAGCATTGGAGAGGTATTAAACCAAAGACGGGGGCACCATATTCATGTGATATTGGCTATG
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gtcatcttttctataagaacttctgacttaaagaaatataggatataaatggtgtaatttcattgatcattgtatagttttatgtccagaattttgaatctggatcttatttgatgatgactcagtttttcaatgattacagGAGTTCAATAAGCATGACAAAGAGCCTGGGAAGTACATAAAGCATTGGAGGGGCATCAAACCGAAGACAGGAGCACCATACTCTTGTGATGTTGGCTATGMapped 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|10238544|gb|BE807432.1|BE807432EST: TCGGAAAGTGAAGGAAATGTATTGCTACACCTTGCTCTGACATTGTGAAG GAATTTAATAAGCATGACAAAGAACCAGGCAAGTACATCAAGCATTGGAGA
genomic: TCGGAAAGTGAAGGAAATGTATTGCTACACC-TGCTCTGACATTGTGAAGgttgtcttta ... tttctctcagGAATTTAATAAGCATGACAAAGAACCAGGCAAGTACATCAAGCATTGGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtggtcttttaaatttttagttttcctacataacattagctaaatttctctcagGAATTTAATAAGCATGACAAAGAACCAGGCAAGTACATCAAGCATTGGAGAGGTATTAAACCAAAGACGGGGGCACCATATTCATGTGATATTGGCTATG
agctaaa putative branch site (score: 3)
tttctctc CT-rich tract
ttttaaatttttagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctttaatttgcccttctttttgtgaatcaagggatgtaactaaagtggtcttttaaatttttagttttcctacataacattagctaaatttctctcagGAATTTAATAAGCATGACAAAGAACCAGGCAAGTACATCAAGCATTGGAGAGGTATTAAACCAAAGACGGGGGCACCATATTCATGTGATATTGGCTATG
- - - - - - cccttct
- - - - - - - - - -ttttgtg