Sequence
atgc intronic sequence ATGC exonic sequence...actatattttctgcaaatattttcttttatactaataaatactatacattgttcccaacatttttgtgctggtgaaaatcacattctgttgctaatgaagGTATTATGATGATTCTGCCTGTGTTCTGCGGAAGATGTTGTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCGCCAACTTTACCTTGGAAAGTA
Basic information
species | Glycine max |
transcript | GLYMA19G02260.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g48300.1 (Oryza sativa), 3'ss of exon 11
actatattttctgcaaatattttcttttatactaataaatactatacattgttcccaacatttttgtgctggtgaaaatcacat---tctgttgctaatgaagGTATTATGATGATTCTGCCTGTGTTCTGCGGAAGATGTTGTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCGCCAACTTTACCTTGGAAAGTA
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---gtaatttatttaatcctagtgttcttttcttacaga--ctgtctatggaccttaa----ttagttctga-aagatttgcgtaagtttttctatcattcagGTATTATGACGATGCTGCATGCATCTTACGAAAGATATTTCTAGATGCAAAGGCACCTCATCTTTCTTCAACCATCCCTCCAAGCCTTCCTTGGAAATCT
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 12
actatattttctgcaaatattttcttttatactaataaatactatacattgttcccaac-atttttgtgctggtgaaaatcac--attctgttgctaatgaagGTATTATGATGATTCTGCCTGTGTTCTGCGGAAGATGTTGTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCGCCAACTTTACCTTGGAAAGTA
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--gataaacactgtgt-catcgtcatatccacttttggaactctcagtttgtattcatttggagttttaatcagaaatgtcaccagatctctttctctgtaagGTATTACGACGATGCTGCTTGTGTGCTACGGAAAATGTTTTTGGATGCAAAGGCTCCTCATCTTTCTTCAACAATTCCTCCCATTCTGCCATGGAAAATC
upper sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 11
----actatattttctgcaaatattttcttttatactaataaatactatacattgttcccaacattt-ttgtgctggtgaaaatcacattctgttgctaatgaagGTATTATGATGATTCTGCCTGTGTTCTGCGGAAGATGTTGTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCGCCAACTTTACCTTGGAAAGTA
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ttttgacatatattctt----tactccattttcatcttactatttcaata-atcattttttgtgttggttgtaaaaatgtacacggtatctctttccaactacagGTATTATGATGATGCTGCTTGTGTGTTGAGGAAGATGTTTATAGACGCGAAGGCCCCTCATCTTTCTTCAACAATTCCACCAACTTTACCTTGGAAGGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acattgttcccaacatttttgtgctggtgaaaatcacattctgttgctaatgaagGTATTATGATGATTCTGCCTGTGTTCTGCGGAAGATGTTGTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCGCCAACTTTACCTTGGAAAGTA
tgctaat putative branch site (score: 2)
aacattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actatattttctgcaaatattttcttttatactaataaatactatacattgttcccaacatttttgtgctggtgaaaatcacattctgttgctaatgaagGTATTATGATGATTCTGCCTGTGTTCTGCGGAAGATGTTGTTAGATGCAAAAGCACCTCATCTTTCTTCAGCAATTCCGCCAACTTTACCTTGGAAAGTA
- - - - ttctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacattc