Sequence
atgc intronic sequence ATGC exonic sequencegttgaattagaaggttcaatcttagttttgttgacataatttctccgccaccttaaagttgttgtaactttgctagttgcaacaaattttgctttctagtccattttgtctcatttgtctattattttggtttagAGTTCTAGGTGGCCTTCTCAGTGCTTATGATCTCTCTGGTGACAAAGTTTTCCTTGAGAAGGCTAAAGATCTTGCAGATAAGTTATTACCTGCTTGGAAT
Basic information
species | Glycine max |
transcript | GLYMA17G06600.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G06600.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 5
gttgaattagaaggttcaatcttagt------tttgttgacataatttctccgccaccttaaa--gttgttgta-------actttgctagttgcaacaaattttgctttctagtccattttgtctcatttgtctattattttggtttagAGTTCTAGGTGGCCTTCTCAGTGCTTATGATCTCTCTGGTGACAAAGTTTTCCTTGAGAAGGCTAAAGATCTTGCAGATAAGTTATTACCTGCTTGGAAT
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gttgccttataaggtttactattgttgtagtattttttttcttaaaatatttgacttctttgatcgatgctatgtaggcagaccacattttttagaacataaaagtatatctagttttttctaagtttctgttttatttttata-ttcagAGTTGTTGGAGGCCTCCTCAGTGCATATGATCTATCTGGTGACAAAGTATTTCTTGAGAAGGCCAAAGATATTACTGACCGTCTACTACCTGCTTGGGAT
upper sequence: GLYMA17G06600.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G128914_T02 (Zea mays), 3'ss of exon 5
gttgaattagaaggttcaatcttagttt--tgttgacataatttctc-cgcca-------ccttaaagttgtt------gtaactttgctagttgcaacaa-attttgctttcta---------------gtccattttgtctcattt---gtctattattttggtttagAGTTCTAGGTGGCCTTCTCAGTGCTTATGATCTCTCTGGTGACAAAGTTTTCCTTGAGAAGGCTAAAGATCTTGCAGATAAGTTATTACCTGCTTGGAAT
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gttgcattataaggtttacctttattacagtatttgtttatcttctcatattagtttgttccttgcagatgtttggctgaaaaagccaatggatgcaccttcattatgatccctatagaaaaataactacagctaggttgtctaattttattttctttgtttgtattcagGGTTGTTGGAGGTTTGCTTAGTGCATATGATCTATCTGGTGATAAAGTATTTCTTGATAAGGCTAAAGATATTACAGATCGTCTATTACCTGCTTGGGAT
upper sequence: GLYMA17G06600.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 5
gttgaattaga-aggttcaatcttagttttgttgacataatttct------ccgccaccttaaagttgttgtaactttgctagttgcaacaaattttgctttctagtc---cattttgtctcatttgtctattattt--tggttt--agAGTTCTAGGTGGCCTTCTCAGTGCTTATGATCTCTCTGGTGACAAAGTTTTCCTTGAGAAGGCTAAAGATCTTGCAGATAAGTTATTACCTGCTTGGAAT
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gttgcatttaacaggtttaccatgttttttttctacatgtactaagaagagtcatcttgtttaggttatctgttgtgtgtagttaacaaaatatgtggtatggaagtgtggcatctgtgcttatatattttctctttgttggctttcagAGTGGTAGGAGGGCTTCTCAGTGCGTATGATCTTTCTGGGGATAAAATTTTCCTTGAAAAGGCTATGGATATTGCAGACAGATTATTGCCTGCATGGGAC
upper sequence: GLYMA17G06600.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0052g00140.t01 (Vitis vinifera), 3'ss of exon 5
gttgaattagaaggttcaatcttagtt------ttgttgacataatttctccgccacctt-----aaagttgttgtaactttgctagttgcaacaaa------ttttgctt-tctagtccattttgtctcatttgtcta-ttattttggtt-tagAGTTCTAGGTGGCCTTCTCAGTGCTTATGATCTCTCTGGTGACAAAGTTTTCCTTGAGAAGGCTAAAGATCTTGCAGATAAGTTATTACCTGCTTGGAAT
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gttgcattataaggtttcatcttatttatttatttaataataagtttctttttttttctttggggacagaggtcctctctgggatggttgagaggaagaagcgtatgacatgtccactgctttttatcctttttgtatacttatgttgaatgcagAGTTTTAGGTGGACTTCTTAGTGCATATGATCTTTCCGGTGACAAAGTCTTCCTTGAAAAGGCTCAAGATATTGCAGATAGATTGCTGCCTGCTTGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacaaattttgctttctagtccattttgtctcatttgtctattattttggtttagAGTTCTAGGTGGCCTTCTCAGTGCTTATGATCTCTCTGGTGACAAAGTTTTCCTTGAGAAGGCTAAAGATCTTGCAGATAAGTTATTACCTGCTTGGAAT
ttatttt CT-rich tract
atttgtctattatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgaattagaaggttcaatcttagttttgttgacataatttctccgccaccttaaagttgttgtaactttgctagttgcaacaaattttgctttctagtccattttgtctcatttgtctattattttggtttagAGTTCTAGGTGGCCTTCTCAGTGCTTATGATCTCTCTGGTGACAAAGTTTTCCTTGAGAAGGCTAAAGATCTTGCAGATAAGTTATTACCTGCTTGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT