Sequence
atgc intronic sequence ATGC exonic sequence...actaaactgacttcataatttgattttaagtctgtatgttacctttaactctaaaagtctaatggtgatgaaatgatttatgactgagtttctattacagGTCCTGTTATGACCAAATTCACCATAGCCTTACGAGAAATTGGTACATACAAGGAAGTTCTTCGATCACAG
Basic information
species | Glycine max |
transcript | GLYMA08G28890.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 3
actaaactgacttcataatt--tgattttaagtctgtatgttacctttaactctaa-aagtctaatggtgatgaaatgatttatgactgagtttctattacagGTCCTGTTATGACCAAATTCACCATAGCCTTACGAGAAATTGGTACATACAAGGAAGTTCTTCGATCACAG
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---cttttcatcccttaattactgttttcattttactagaactgtcttgtctttagtatggtcatttcctctaatatgcatactgaacatttctcctctccagGACCTGTTATGACCAAATTTACAATTGCCTTGAGAGAACTAGGCACATACAAGGAAGTCCTCCGCTCCCAG
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM5G872204_T02 (Zea mays), 3'ss of exon 3
actaaactgacttcataatttgattttaagtctgtat---gttacctttaactctaaaagtctaatggtgatgaaatgatttatgactgagtttctattacagGTCCTGTTATGACCAAATTCACCATAGCCTTACGAGAAATTGGTACATACAAGGAAGTTCTTCGATCACAG
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tttctcattatttattactctttccccacataagagtagagttgagctcaatgtcgtcagttcctc--tactgagcatactgaattttcatcttct-ttccagGGCCTGTAATGACCAAATTTACAATTGCCTTAAGAGAAATTGGAACATACAAGGAAGTCCTGCGCTCCCAG
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 3
-----------------------------------------------actaaactgacttcataatttgattttaagtctgtatgtt---acctttaactctaaaagtctaatggtgatgaaatgatttatgac-tgagtttctattacagGTCCTGTTATGACCAAATTCACCATAGCCTTACGAGAAATTGGTACATACAAGGAAGTTCTTCGATCACAG
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gttagtaatgtggttctcgtgaaaatacatgtattcgaaacttcaatttgtgacaagcatgataactctttctcctgttttcatgttttgcccttttgctttcctgattggttggttctcttgtacatgacaacatttaccttttttgcagGGCCTGTCATGACCAAATTTACAATTGCTTTAAGAGAAATTGGAACATACAAGGAAGTATTGCGCTCCCAG
upper sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 3
actaaactg---acttcataatttgattttaagtctgtatgttacctttaactctaaaagtctaatggtgatgaaatgatttatgactgagtttctattacagGTCCTGTTATGACCAAATTCACCATAGCCTTACGAGAAATTGGTACATACAAGGAAGTTCTTCGATCACAG
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-tttaactggaaattgcatgatatggtactagctcctagaaggcctgttcataagtgaaatttactggcattgt--tgatgaaatctctatttgtttcttcagGCCCTGTTATGACCAAATTCACTATTGCATTGAGAGAGATTGGGACATACAAGGAAGTTCTTCGCTCCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taactctaaaagtctaatggtgatgaaatgatttatgactgagtttctattacagGTCCTGTTATGACCAAATTCACCATAGCCTTACGAGAAATTGGTACATACAAGGAAGTTCTTCGATCACAG
gtctaat putative branch site (score: 3)
tttctatt putative PPT
atgaaatgatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actaaactgacttcataatttgattttaagtctgtatgttacctttaactctaaaagtctaatggtgatgaaatgatttatgactgagtttctattacagGTCCTGTTATGACCAAATTCACCATAGCCTTACGAGAAATTGGTACATACAAGGAAGTTCTTCGATCACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - ctgactt
- - - - - - - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgagtt