Sequence
atgc intronic sequence ATGC exonic sequence...atgtccgcagtaaagaaagtactttcgtgtcaagaaatcgttgctagatcttaagatgctatgttcagtgtattgacagctggatcaattctctctgtagATGGGAAAATTCTATGAGATGTTTGAAATGGATGCACATATCGGTGCGAAGGAGCTGGACTTGCAGTATATGAAG
Basic information
species | Physcomitrella patens |
transcript | PP1S152_6V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S152_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os09g24220.1 (Oryza sativa), 3'ss of exon 4
atgtccgcagtaaagaaagtactttcgtgtcaagaaatcgttgctagatcttaagatgctatgttcagtgtattgacagctggatcaattctctctgtagATGGGAAAATTCTATGAGATGTTTGAAATGGATGCACATATCGGTGCGAAGGAGCTGGACTTGCAGTATATGAAG---------------------------------------------------------------------------------
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---------gtacaacta-tatttt-gtaacagttgtggaatactaaagttaaggctaccttgtttagtaaat-----attctatgaatttgaa--atagatgggcaaattctatgaattatttgaaatggatgcacatgttggggcaaaggagcttgatcttcagtatatgaaggtagtaaattctcttctgcttattcagTATACTGCTGTCACTGCACAATCCAGCTTTTGTTTTAATTCTTATGGCATAACG
upper sequence: PP1S152_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA19G40350.1 (Glycine max), 3'ss of exon 4
atgtccgcagtaaagaaagtactttcgtgtcaagaaatcgttgctagatcttaagatgctatgttcagtgtattgacagctggatcaattctctctgtagATGGGAAAATTCTATGAGATGTTTGAAATGGATGCACATATCGGTGCGAAGGAGCTGGACTTGCAGTATATGAAG
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--gtttgagttggttaagttttgttggtgccattattccattcctta----caagttacaac--caaatgaaatatttttcctccctattgttgatgcagATGGGTAAATTTTATGAGCTTTTTGAGATGGATGCACATGTAGGTGCGAAAGAGCTTGACTTGCAGTATATGAAG
upper sequence: PP1S152_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA03G37750.1 (Glycine max), 3'ss of exon 2
atgtccgcagtaaagaaagtactttcgtgtcaagaaatcgttgctagatcttaagatgctatgttcag-tgtattgacagctggatcaattctctctgtagATGGGAAAATTCTATGAGATGTTTGAAATGGATGCACATATCGGTGCGAAGGAGCTGGACTTGCAGTATATGAAG
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--gtttgagttggctaagttttgttggtgccattagtccatt------tccttacaagttatgaccaaatgaaatatttttcctccctattgttggtgcagATGGGTAAATTTTATGAGCTTTTTGAGATGGATGCACATGTAGGTGAGAAAGAGCTTGACTTGCAGTATATGAAG
upper sequence: PP1S152_6V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT4G02070.2 (Arabidopsis thaliana), 3'ss of exon 4
atgtccgcagtaaagaaagtactttcgtgtcaagaaatcgttgctagatcttaagatgctatgttcagtgtattgacagctggatcaattctctctgtagATGGGAAAATTCTATGAGATGTTTGAAATGGATGCACATATCGGTGCGAAGGAGCTGGACTTGCAGTATATGAAG
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------gtagaacgataattacttatttcgttataacttatttattgatgg-gagattctaggataaatg-gtcttcttttgtggcaa--------gcagATGGGTAAATTCTATGAGCTTTTTGAGATGGATGCACATGTCGGAGCTAAGGAACTGGATATACAATACATGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatcttaagatgctatgttcagtgtattgacagctggatcaattctctctgtagATGGGAAAATTCTATGAGATGTTTGAAATGGATGCACATATCGGTGCGAAGGAGCTGGACTTGCAGTATATGAAG
tattgac putative branch site (score: 2)
ttctctctgt putative PPT
ttaagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtccgcagtaaagaaagtactttcgtgtcaagaaatcgttgctagatcttaagatgctatgttcagtgtattgacagctggatcaattctctctgtagATGGGAAAATTCTATGAGATGTTTGAAATGGATGCACATATCGGTGCGAAGGAGCTGGACTTGCAGTATATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA