Sequence
atgc intronic sequence ATGC exonic sequence...tatccagggattcgcacattgagttcttggatacaacgtttgaaattactccctgaattaaggcgcgtacttcttttgtttactattggtaattatgcagGTGTGCGAGAGGCTGGGGCCAAGTTTGTACGATTTTCTTCGAAAAAACAATTATCGACCGTTTTCTGCAGATCTTGTTCGAGATTTTGGCCGCCAACTCT
Basic information
species | Physcomitrella patens |
transcript | PP1S425_6V6.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S425_6V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA17G13440.2 (Glycine max), 3'ss of exon 4
tatccagggattcgcacattga-gttcttggatacaacgtttgaaattactccctgaattaaggcgcgtacttcttttgtttactattggtaattatgcagGTGTGCGAGAGGCTGGGGCCAAGTTTGTACGATTTTCTTCGAAAAAACAATTATCGACCGTTTTCTGCAGATCTTGTTCGAGATTTTGGCCGCCAACTCT
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---gtaagtatttaatttgtgatggaatcatttccccaatttacaaataatttgggggttaagaca-acagtgaattta------aatggt--tttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAGACAACTAT
upper sequence: PP1S425_6V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA05G02740.3 (Glycine max), 3'ss of exon 4
tatccagggattcgcacattgagttcttg--gatacaacgtttgaaattactccctgaattaaggcgcgtacttcttttgtttactattggtaattatgcagGTGTGCGAGAGGCTGGGGCCAAGTTTGTACGATTTTCTTCGAAAAAACAATTATCGACCGTTTTCTGCAGATCTTGTTCGAGATTTTGGCCGCCAACTCT
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-----------gtaagtatttaatttgtgatggaatcatttccccaatttacaaataatttgggggttaagacaacggtgaatttaaatggt--tttaacagGTGTTTGAGAAACTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCCATTGATCTTGTCCGTGAGATTGGCAAACAACTAT
upper sequence: PP1S425_6V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 4
tatccagggattcgcacattgagttcttggatacaacgtttgaaattactccctgaattaaggcgcgtacttcttttgtttactattggtaatta-tgcagGTGTGCGAGAGGCTGGGGCCAAGTTTGTACGATTTTCTTCGAAAAAACAATTATCGACCGTTTTCTGCAGATCTTGTTCGAGATTTTGGCCGCCAACTCT
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---gtaagtatttagtcaattttgtgatgtctatgattttccccggtttgggaaatagttggggttgaattttgtggatgaacttaaaatggttgctacagGTATTTGAGAAGCTTGGATCGAGTTTATACGATTTTCTTCGGAAAAACAATTATCGCTCCTTTCCCATTGATCTTGTCCGTGAGATTGGCTGGCAACTCT
upper sequence: PP1S425_6V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 5
tatccagggattcgcacattgagttcttggatacaacgtttgaaattactccctgaat--taaggcgcgtacttctt-ttgtttactattggtaattatg-cagGTGTGCGAGAGGCTGGGGCCAAGTTTGTACGATTTTCTTCGAAAAAACAATTATCGACCGTTTTCTGCAGATCTTGTTCGAGATTTTGGCCGCCAACTCT
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---gtaagtatatg---actgatttac--gatgatatgatttccccaacttcatgaatattttggggcttaaaacttgttagtgaatttaaatggtcttaacagGTATTTGAGATGCTTGGACCAAGCTTATACGATTTTCTTCGGAAAAACAATTATCGCTCATTTCCAGTTGATCTAGTCCGCGAGATTGGCAGACAACTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttactccctgaattaaggcgcgtacttcttttgtttactattggtaattatgcagGTGTGCGAGAGGCTGGGGCCAAGTTTGTACGATTTTCTTCGAAAAAACAATTATCGACCGTTTTCTGCAGATCTTGTTCGAGATTTTGGCCGCCAACTCT
ttttgtttactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatccagggattcgcacattgagttcttggatacaacgtttgaaattactccctgaattaaggcgcgtacttcttttgtttactattggtaattatgcagGTGTGCGAGAGGCTGGGGCCAAGTTTGTACGATTTTCTTCGAAAAAACAATTATCGACCGTTTTCTGCAGATCTTGTTCGAGATTTTGGCCGCCAACTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT