Sequence
atgc intronic sequence ATGC exonic sequencegtattaacttcactatatttgaaagcaattcctgtcgcgttctcttatttcctcgcttgctctgccaccgttttctccaacattttgataatgatgtgggcgttcttgtagGGGTCCAGGTATCCTAATGCTCATTCTGTCATGGATCATCACCCTCTTCACTCTCTGGCAGATGGTGGAAATGCACGAAGCTGTCCCGGGTAGGCGGTTT
Basic information
species | Physcomitrella patens |
transcript | PP1S105_62V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S105_62V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os08g03350.1 (Oryza sativa), 3'ss of exon 2
gtattaacttcactatatttgaaagcaattcctgtcgcgttctcttatttcctc-gcttgctctgccaccgttttctccaacattttgat---aatga-tgtgggcgttcttgtagGGGTCCAGGTATCCTAATGCTCATTCTGTCATGGATCATCACCCTCTTCACTCTCTGGCAGATGGTGGAAATGCACGAAGCTGTCCCGGGTAGGCGGTTT
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------------------------gtcagtcctactatcttcttcatcttcatctgaacgaagaacacacgaacgaaccaagaaattaatctaactgaattcttgaatttttgcagGGGACCTGGCATCGCGGTGCTGATCCTGTCATGGATCATCACGCTCTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGGAAGCGGTTC
upper sequence: PP1S105_62V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G127338_T02 (Zea mays), 3'ss of exon 1
gtattaacttcactatatttgaaagcaattcctgtcgcgttctcttatttcctcgcttgctctgccaccgttttctccaacattttgata--atgatgtgggcgttcttgtagGGGTCCAGGTATCCTAATGCTCATTCTGTCATGGATCATCACCCTCTTCACTCTCTGGCAGATGGTGGAAATGCACGAAGCTGTCCCGGGTAGGCGGTTT
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----------------gtgcgtacgctagcttgctagctgtgtgcctgtgtctgactgactctgagcgcgcttaaattagatgtatcatatcatgccatgcatgcatatgcagGGGCCCCGGCATCGCGGTGCTGCTGCTGTCGTGGATCATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTCCCGGGCAAGCGCTTC
upper sequence: PP1S105_62V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G149216_T01 (Zea mays), 3'ss of exon 2
gtattaacttcactatatttgaaagcaattcctgtcgcgttctcttatttcctcgcttgctctgccaccgttttctccaacattttgataatgat-gtgggcgttcttgtagGGGTCCAGGTATCCTAATGCTCATTCTGTCATGGATCATCACCCTCTTCACTCTCTGGCAGATGGTGGAAATGCACGAAGCTGTCCCGGGTAGGCGGTTT
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----tgattcaattgtac----gagcgatt---aactcgttgtcagataaagattattagggggtcacgggcagata-aatggttcattgttgattattggcgtgcacacagGGGCCCTGGCATCGCGGTGATGATCCTGTCGTGGATAATCACCCTATACACGCTATGGCAGATGGTGGAGATGCACGAGATGGTGCCTGGGAAGCGGTTC
upper sequence: PP1S105_62V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA16G06750.1 (Glycine max), 3'ss of exon 1
--gtattaacttcactatatttgaaagcaattcctgtcgcgttctcttatttcctcgcttgctctgccaccgttttctccaacattttgataatgatgtgggcgttcttgtagGGGTCCAGGTATCCTAATGCTCATTCTGTCATGGATCATCACCCTCTTCACTCTCTGGCAGATGGTGGAAATGCACGAAGCTGTCCCGGGTAGGCGGTTT
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cttccatgacctcaaagaaataaaaaaagataaacaactttttagtatatatacta---tactatgc----gtttttt-----aatttgagaatcac-tatgttttttttcagGGGTCCTGGTGTAACTGTACTAATCCTGTCATGGATCATCACCCTGTACACTCTATGGCAAATGGTTGAGATGCATGAAATGGTACCTGGAAAACGTTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgctctgccaccgttttctccaacattttgataatgatgtgggcgttcttgtagGGGTCCAGGTATCCTAATGCTCATTCTGTCATGGATCATCACCCTCTTCACTCTCTGGCAGATGGTGGAAATGCACGAAGCTGTCCCGGGTAGGCGGTTT
ttttgat putative branch site (score: 4)
cgttctt putative PPT
aacattttgataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattaacttcactatatttgaaagcaattcctgtcgcgttctcttatttcctcgcttgctctgccaccgttttctccaacattttgataatgatgtgggcgttcttgtagGGGTCCAGGTATCCTAATGCTCATTCTGTCATGGATCATCACCCTCTTCACTCTCTGGCAGATGGTGGAAATGCACGAAGCTGTCCCGGGTAGGCGGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG