Sequence
atgc intronic sequence ATGC exonic sequence...tcatttgccactatcaaatatgccaatgctgttcatgattttgccatacttttctgcaaatgacccgagattagtttttcacctctgctagtctttacagTGCAGCTTCAACATCATGCACGGCATCGCCTGCCAACATTTCAGCTGATCTTTGTACATGTGATTGAATCACTAGTTTTTGTTCCT
Basic information
species | Glycine max |
transcript | GLYMA08G19970.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g45770.1 (Oryza sativa), 3'ss of exon 9
--------------tcatttgccactatcaaatatgcca-atgct--gttcatgattttgccatacttttctgcaaatgacccgagattagtttttcacctctgctagtctttacagTGCAGCTTCAACATCATGCACGGCATCGCCTGCCAACATTTCAGCTGATCTTTGTACATGTGATTGAATCACTAGTTTTTGTTCCT
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gtttgtgcttattgctttacgttgtttcttggcctgctagatgctcaacttgttattatgatattatcttatggtaataa----ataatattttgttttcttcattgaaaatttcagTGCAGCTTCAACATCATGCACGCCACCAACTCCCCACATTTCAACTGATATTTGTCCATGTTATCGAATCATTGGTTTTTGTTCCG
upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g45770.2 (Oryza sativa), 3'ss of exon 9
--------------tcatttgccactatcaaatatgcca-atgct--gttcatgattttgccatacttttctgcaaatgacccgagattagtttttcacctctgctagtctttacagTGCAGCTTCAACATCATGCACGGCATCGCCTGCCAACATTTCAGCTGATCTTTGTACATGTGATTGAATCACTAGTTTTTGTTCCT--------------
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gtttgtgcttattgctttacgttgtttcttggcctgctagatgctcaacttgttattatgatattatcttatggtaataa----ataatattttgttttcttcattgaaaatttcagTGCAGCTTCAACATCATGCACGCCACCAACTCCCCACATTTCAACTGATATTTGTCCATGTTATCGAATCATTGGTTTTTGTTCCGGTATGATATTTTTT
upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G60995.1 (Arabidopsis thaliana), 3'ss of exon 10
tcatttgccactatcaaatatgccaatgctgttcatgattttgccatacttttctgcaaatgacccgagattagtttttcacctctgctagtctttacagTGCAGCTTCAACATCATGCACGGCATCGCCTGCCAACATTTCAGCTGATCTTTGTACATGTGATTGAATCACTAGTTTTTGTTCCT
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--gttag--aatttcttctattccaata--gcttatggtttc-caatctttgcttctcaacaatc----atctttgtttcgatatcact--ttgttgcagTGCAGCTTCAACACCATGCCCAGCATCGGTTACCAACATTTCAGTTGATCTTTGTACACGTGATCGAATCGCTTGTCTTTGTACCG
upper sequence: GLYMA08G19970.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0034g02140.t01 (Vitis vinifera), 3'ss of exon 9
tcatttgccactatcaaatatgccaatgctgttcatga----ttttgccat-acttttctgcaaatgacccgagattagtttttcacctctgctagtctttacagTGCAGCTTCAACATCATGCACGGCATCGCCTGCCAACATTTCAGCTGATCTTTGTACATGTGATTGAATCACTAGTTTTTGTTCCT
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---tctggactgatgtatgatccataggttacacacaaagagcaatgtcatcagttcttttctttctctgtgtgatt-gtgtctcattt-tctcaattattgcagTGCAGCTTCAACACCATGCTAGACATCGGCTTCCAACATTCCAGTTGATCTTTGTACACGTGATTGAATCCCTTGTCTTTGTACCAMapped 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|5606329|gb|AI900427.1|AI900427EST: AGTATCATTTACATTAAGAGAAACACAGACTCGCATGCTGAAGTTCACGG TGCAGCTTCAACATCATGCACGGCATCGCCTGCCAACATTTCAGCTGATCT
genomic: AGTATCATTTACATTAAGAGAAACACAGACTCGCATGCTGAAGTTCACGGgtaggattgt ... gtctttacagTGCAGCTTCAACATCATGCACGGCATCGCCTGCCAACATTTCAGCTGATCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacttttctgcaaatgacccgagattagtttttcacctctgctagtctttacagTGCAGCTTCAACATCATGCACGGCATCGCCTGCCAACATTTCAGCTGATCTTTGTACATGTGATTGAATCACTAGTTTTTGTTCCT
tctttac CT-rich tract
attagttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatttgccactatcaaatatgccaatgctgttcatgattttgccatacttttctgcaaatgacccgagattagtttttcacctctgctagtctttacagTGCAGCTTCAACATCATGCACGGCATCGCCTGCCAACATTTCAGCTGATCTTTGTACATGTGATTGAATCACTAGTTTTTGTTCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - -tgccact
- - - - - - - - - tatgcca
- - - - - - - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - -catgatt
- - - - - - - - - - - - - - - - - - - - - -ccatact
- - - - - - - - - - - - - - - - - - - - - - - - - -ttctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgaccc