Sequence
atgc intronic sequence ATGC exonic sequence...gaagtaattaagtgattattaattcatggaaactgtatactagttgtagtgattgatttctggctactcttctcatcttttgtgtttggctgaagagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAGACGAAATTTGTTCTTGCAAAGGCCTTGA
Basic information
species | Glycine max |
transcript | GLYMA12G14080.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G14080.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G31060.3 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------------------------------------------------------gaagtaattaag--tgattattaattcatggaaact-gtatactagttgtagtgattgatttctggctactcttctcatcttttgtgtttggctgaagagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAGACGAAATTTGTTCTTGCAAAGGCCTTGA
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gtatgatactgatcttacttttagcgtattatttgattctcatgctcgtttttagtagaaatgcatattagtggacaaaagataaattaattagaagttctcaatacctactcatggtctgttgacattaggatactccttactgtagaacataggtg-ctatctttgtgactattt-tgtgtatttgaattatagGTTGAACGAGTCGTTGGTATGGTTGAAGGAGCTATATTAGTTGTTGATGCTGGAGAAGGCCCTCTTGCACAGACTAAGTTTGTTCTTGCCAAAGCCTTGA
upper sequence: GLYMA12G14080.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G31060.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------------------------------gaagtaattaag--tgattattaattcatggaaact-gtatactagttgtagtgattgatttctggctactcttctcatcttttgtgtttggctgaagagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAGACGAAATTTGTTCTTGCAAAGGCCTTGA
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gtgaggtatgatactgatcttacttttagcgtattatttgattctcatgctcgtttttagtagaaatgcatattagtggacaaaagataaattaattagaagttctcaatacctactcatggtctgttgacattaggatactccttactgtagaacataggtg-ctatctttgtgactattt-tgtgtatttgaattatagGTTGAACGAGTCGTTGGTATGGTTGAAGGAGCTATATTAGTTGTTGATGCTGGAGAAGGCCCTCTTGCACAGACTAAGTTTGTTCTTGCCAAAGCCTTGA
upper sequence: GLYMA12G14080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0028g02640.t01 (Vitis vinifera), 3'ss of exon 2
gaagtaa---ttaagtgattattaattcatggaaactgtatactagttgtagtgattgatttctg-gctactcttctcatcttttgtgtttggctgaagagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAGACGAAATTTGTTCTTGCAAAGGCCTTGA
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ggtgtaagctttacttacacactggtt--tgcaagttttcttgtttttattttgctagatcactaagttgatccttgtataattacttttt--ctgttggttagGTTGAGCGGGTTGTTGGCATGGTTGAAGGAGCAGTTTTAGTTGTAGATGCTGGTGAAGGTCCCCTTGCACAAACAAAGTTTGTCCTTGCAAAAGCCTTAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtagtgattgatttctggctactcttctcatcttttgtgtttggctgaagagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAGACGAAATTTGTTCTTGCAAAGGCCTTGA
gattgat putative branch site (score: 4)
attgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaagtaattaagtgattattaattcatggaaactgtatactagttgtagtgattgatttctggctactcttctcatcttttgtgtttggctgaagagtagGTTGAGCGTGTTGTTGGTATGGTTGAGGGAGCGATTTTGGTTGTTGATGCTGGTGAAGGTCCACTTGCACAGACGAAATTTGTTCTTGCAAAGGCCTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - catggaa
- - - - - - - - - - - - - - - - - - - - - - tgtagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctggc