Sequence
atgc intronic sequence ATGC exonic sequence...cgagtagcgtaggaagcacttgcaagcggcttggtgttgcggggattgggatggcgttgtaaagcgtgagatgagtgggggatgtggcatggaagttcagGTTTCTGGCGTGAACGAGGATCATGTGAAGCAGATCACGGAGCTGAAGCTGTCTGTGGAGAGTCTGGAGAAGGAGCGCGACTTTTACTTTACGAAGCTGC
Basic information
species | Physcomitrella patens |
transcript | PP1S49_111V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S49_111V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ09412 (Selaginella moellendorffii), 3'ss of exon 5
---------------------------------------------cgagtagcgt-aggaagcacttgcaagcggc--ttggtgttgcggggattgggatggcgttgtaaagcgtgagatgagtgggggatgtggcatggaagtt--cagGTTTCTGGCGTGAACG-----AGGATCATGTGAA---GCAGATCACGGAGCTGAAGCTGTCTGTGGAGAGTCTGGAGAAGGAGCGCGACTTTTACTTTACGAAGCTGC
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gtaagctcctggttacacggctatcaatcactgatacattttttacagttaaaaccaagcaactaatgtcagcagcagtcgtcgtccctcctactggatcggctccacaaacgccagccagactttatgctcttcaagAACAGGTACTTGGCAACTTGTTCCAACGTCTTCATACCTACTTGATTTCGCAGATCACGGAGCTCAAGCTGTCAGTGGACAGTCTCGAGAAAGAGAGGGA--------------------
upper sequence: PP1S49_111V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ34606 (Selaginella moellendorffii), 3'ss of exon 5
-----------------------------------------------------------cgagtagcgtaggaagcacttgcaagcggcttggtgttgcggggattgggatggcgtt-gtaaagcgtgagatgagtgggggatgtg-gcatggaagttcagGTTTCTGGCGTGAACGAGGATCATGTGAAGCAGATCACGGAGCTGAAGCTGTCTGTGGAGAGTCTGGAGAAGGAGCGCGACTTTTACTTTACGAAGCTGC
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gtaagctcctggttacacggctatcaatcactgatacattttttacagttaaaaccaagcaactaatgtctgcagcagtcgtcgtc--cctcctactggatcggctccacaaacgccagccagactttatgctcttcaagAACAGGTACTTGGCAACTT-GTTCCAACGTCTTCATACCTACTTGATTTCGCAGATCACGGAGCTCAAGCTGTCAGTGGACAGTCTCGAGAAAGAGAGGGA-------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgggatggcgttgtaaagcgtgagatgagtgggggatgtggcatggaagttcagGTTTCTGGCGTGAACGAGGATCATGTGAAGCAGATCACGGAGCTGAAGCTGTCTGTGGAGAGTCTGGAGAAGGAGCGCGACTTTTACTTTACGAAGCTGC
ttgtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgagtagcgtaggaagcacttgcaagcggcttggtgttgcggggattgggatggcgttgtaaagcgtgagatgagtgggggatgtggcatggaagttcagGTTTCTGGCGTGAACGAGGATCATGTGAAGCAGATCACGGAGCTGAAGCTGTCTGTGGAGAGTCTGGAGAAGGAGCGCGACTTTTACTTTACGAAGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - cacttgc