Sequence
atgc intronic sequence ATGC exonic sequence...ttataaacagggattttgtctgaaagaatcccttagtctgcataacttaatttttcttgatgccttgtttaaccaacatttctttcattcttgaccatagTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG
Basic information
species | Glycine max |
transcript | GLYMA11G15020.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 2
ttataaacagggattttgtctgaaagaatcccttagtctgcataacttaatttttcttgatgccttgtttaaccaacatttctttcat--tcttgaccata--gTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG-------------
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--acattcattacccgtgg-tgatgcaacaactatactaacacaaatca-ctatgatccatgtagtggtagaaattgatttgttgaatgattttgaaaatacagTCGAATATGAGGATCTTGGTGACCGGAGGAGCTGGATTCATTGGTTCACATCTCGTTGATAAATTGATGCAAAACGAAAAGAATGAAGTAATCGTTGCGG
upper sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 2
ttataaacagggattttgtctgaaagaatccct-tagtctgcataacttaatttttcttgatgccttgtttaa--ccaacatttctttcattcttgacc-atagTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG
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-tctgcatctgg-ttgtctatgatttagtttgtatagtaaagttgtacta--tgttcttaataagatgtttaaagtgagtgcttttttttttttcattttgcagTCAAATATGAGGATTTTGATCTCAGGAGGAGCTGGATTCATTGGTTCTCACCTTGTTGATAAGCTGATGGAAAACGAAAAGAATGAG
upper sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 1
ttataaacagggattttgtctgaaagaatcccttagtctgc-ataacttaatttttcttgatgccttgtttaa-ccaacatttctttcattc-ttgaccatagTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG
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--acagaatcagatcttggg-gttttattagtttgatctgttgtgactcaaggatgattatgtaattatatgagtttacttttttcttgtttgttttgtgtagCCCAATATGAGGATCTTGATCTCTGGAGGAGCTGGCTTCATTGGTTCTCACTTGGTTGATAAGCTTATGGAAAATGAGAAGAATGAG
upper sequence: GLYMA11G15020.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 2
ttataaacagggattttgtctgaaagaatcccttagtctg--cataacttaatttttcttgatgccttgtttaaccaacatttctttcattcttgaccatagTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG
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-tccaatcatcacattcatgccaacacatcattgcactagatcattacttttattatcttta-actaattcctacagtaattcctttcactcttgatggcagTCCAATATGAGAATATTGGTCACTGGAGGAGCTGGATTCATTGGTTCACATTTGGTGGACAAGCTGATGGAAAATGAAAAGAATGAGMapped 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|192301457|gb|FG994081.1|FG994081EST: CGAAGCAACCTCCCTTGCCATCTCCCTTGCGTTTCTCCAAATTCTATCAG TCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCAC
genomic: CGAAGCAACCTCCCTTGCCATCTCCCTTGCGTTTCTCCAAATTCTATCAGgtgtactatc ... ttgaccatagTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttaatttttcttgatgccttgtttaaccaacatttctttcattcttgaccatagTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG
tcttgac putative branch site (score: 3)
catttctttcattctt CT-rich tract
tttttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttataaacagggattttgtctgaaagaatcccttagtctgcataacttaatttttcttgatgccttgtttaaccaacatttctttcattcttgaccatagTCTAACATGAGAATCTTGATTACGGGAGGAGCTGGATTCATTGGTTCTCACCTAGTTGATAGATTGATGGAAAATGAAAAAAATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - -ttgtctg
- - - - - - - - - - - - - - - - - - - tgcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgcc