Sequence
atgc intronic sequence ATGC exonic sequence...gatttttctgctgtatgtgtgtagatttgtgatggaatggaaattgattgcgctaagtcgaaaatcttgttgaattttgagcggtttgtgttgtgtgcagTTATGAATGTAAGCTTTGTTTGACGCTCCACAACAACGAGGGTAATTATCTGGCTCACACTCAGGGGAAACGGCATCAGACCAACTTGGCGAAACGTGCA
Basic information
species | Physcomitrella patens |
transcript | PP1S318_71V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S318_71V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g15700.1 (Oryza sativa), 3'ss of exon 1
gatttttctgctgtatgtgtgtagatttgtgatggaatggaaattgattgcgctaagtcgaaaatcttgttgaattttgagcggtttgtgttgtgtgcagTTATGAATGTAAGCTTTGTTTGACGCTCCACAACAACGAGGGTAATTATCTGGCTCACACTCAGGGGAAACGGCATCAGACCAACTTGGCGAAACGTGCA
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-gtactgcctcc-cacccgctaaaaccctagctttcttcttcctcgattcggtttgctccc---tcgcgct-aatcccgctcgattt----cgtgtccagCTACGAGTGCAAGCTGTGCCTGACGCTGCACAACAACGAGGGGAACTACCTGGCTCACACGCAGGGGAAGCGGCACCAGACCAACCTCGCCAAGCGTGCC
upper sequence: PP1S318_71V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv08s0007g04710.t01 (Vitis vinifera), 3'ss of exon 1
--gatttttctgctgtatgtgtgtagatttgtgatggaatggaaattgattgcgctaagtcgaaaatct--tgttgaattttgagcggtttgtgttgtgtgcagTTATGAATGTAAGCTTTGTTTGACGCTCCACAACAACGAGGGTAATTATCTGGCTCACACTCAGGGGAAACGGCATCAGACCAACTTGGCGAAACGTGCA
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cagaaaataaccctatatatatata---ctccattctatttggatctcgctattttattttatttttttgtgattttatttttatgtgattgggcaat-tacagCTATGAGTGTAAGCTTTGCCTGACATTGCACAACAACGAGGGCAATTATTTGGCCCACACACAAGGGAAGAGGCATCAGACGAATTTGGCCAAGAGAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattgcgctaagtcgaaaatcttgttgaattttgagcggtttgtgttgtgtgcagTTATGAATGTAAGCTTTGTTTGACGCTCCACAACAACGAGGGTAATTATCTGGCTCACACTCAGGGGAAACGGCATCAGACCAACTTGGCGAAACGTGCA
aattgat putative branch site (score: 4)
ttgaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatttttctgctgtatgtgtgtagatttgtgatggaatggaaattgattgcgctaagtcgaaaatcttgttgaattttgagcggtttgtgttgtgtgcagTTATGAATGTAAGCTTTGTTTGACGCTCCACAACAACGAGGGTAATTATCTGGCTCACACTCAGGGGAAACGGCATCAGACCAACTTGGCGAAACGTGCA
- - - - tgctgta