Sequence
atgc intronic sequence ATGC exonic sequence...tattacattgtttttgttcatgaaatggatacagtccatcaattcttgtctagattattaatccttttctttaaaaatttattgtcctattttattgcagGTTGTGAATTCAACATATGCATTATGGACTTGGCACCGAAATCAAGACAATTACAAAGAAAATGCAGTTGGTGACCAAATATACATTGTGCGACAACCTG
Basic information
species | Glycine max |
transcript | GLYMA19G03220.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G03220.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g17784.1 (Oryza sativa), 3'ss of exon 4
tattacat-tgtttttgttcatgaaatg-gatacagtccatcaattcttgtctagattattaatccttttctttaaaaatttattgtcctattttattgcagGTTGTGAATTCAACATATGCATTATGGACTTGGCACCGAAATCAAGACAATTACAAAGAAAATGCAGTTGGTGACCAAATATACATTGTGCGACAACCTG
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tatttcttatggccaaatttagctgatatgatttatgttatatgttaat-tatatattgggaagtactccaacttcacagttgtca-cgtgtacgagtgcagGTGGTTAATTCTACATATGCATTATGGACATGGCACCGTAACCAGGATGCATATGGAGAAGACAGCGTGGGGGATCAAATCTATATAGTTCGGCAACCGG
upper sequence: GLYMA19G03220.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G014193_T03 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------------------tattacattgtttttgttcatgaaatggatacagtccatcaattcttgtctagattattaatccttttctt--------taaaaatttat---tgt-cctattttattgcagGTTGTGAATTCAACATATGCATTATGGACTTGGCACCGAAATCAAGACAATTACAAAGAAAATGCAGTTGGTGACCAAATATACATTGTGCGACAACCTG
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gtgacttcacttcagtgactccatttcttataatgatccaacatcagagacagctcagccattctacatcttgcattactcatcatga-gttaacgtgcataatgcagaaacttctgtccagtgtttgtatgtgttttaaatctagtttttagttctcatatgcatttgtgtgtgtatgtgcatgaatccagGTCCTGAATTCAACATATGCCTTATGGACATGGCACCGTAACCAGGACGCATATGCAGAGAACAGTGTGGGAGACCAGATCTACATTGTACGACAGCCTG
upper sequence: GLYMA19G03220.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0051g00640.t01 (Vitis vinifera), 3'ss of exon 6
tattacattgtttttgttcatgaaatggatacagtccatcaatt--cttgtctagattattaatccttttctttaaaaatttattgtcctattttat-tgcagGTTGTGAATTCAACATATGCATTATGGACTTGGCACCGAAATCAAGACAATTACAA-AGAAAATGCAGTTGGTGACCAAATATACATTGTGCGACAACCTG
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--ttctaatgtgatc-ttcaagtagttatctctttctattcatttacttgtacagttgttatatccctctcttttaggtcctaatctgtcattccaaacacagGTTGTGAATTCTACATATGCTCTATGGACTTGGCACAGGAATCAGGATATTTACAAGAGGAAAAGCCGC-GGTGACCAAATATACATCGTACGACAACCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtctagattattaatccttttctttaaaaatttattgtcctattttattgcagGTTGTGAATTCAACATATGCATTATGGACTTGGCACCGAAATCAAGACAATTACAAAGAAAATGCAGTTGGTGACCAAATATACATTGTGCGACAACCTG
tattaat putative branch site (score: 2)
tcctatttt putative PPT
tagattattaatcctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tattacattgtttttgttcatgaaatggatacagtccatcaattcttgtctagattattaatccttttctttaaaaatttattgtcctattttattgcagGTTGTGAATTCAACATATGCATTATGGACTTGGCACCGAAATCAAGACAATTACAAAGAAAATGCAGTTGGTGACCAAATATACATTGTGCGACAACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - catgaaa
- - - - - - - - - - - - - - - - - -ccatcaa