Sequence
atgc intronic sequence ATGC exonic sequencegtcagtacaaactcattgcagttttttttttgtttttgtttttttaaagcaatttactcgttgaaagatatcaatagattcagaagtcagaacagagtataggatttgatcaaaaaccccacaacctgacattgaattcgactctgttcatcctcatctaaacatccgatggtctctttcatggaacagAGCTCTGCAAGATCCAGGCCGATTCAAATGAGAAGCAAACCGACTACTACTTCTTCAGTCGCAAGGACAAGAAGTATCCAACTGGCAACCGAGCCAACCG
Basic information
species | Physcomitrella patens |
transcript | PP1S161_73V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S161_73V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G32770.1 (Arabidopsis thaliana), 3'ss of exon 1
gtcagtacaaactcattgcagttttttttttgtttttgtttttttaaagcaatttactcgttgaaagatatcaatagattcagaagtcagaacagagtataggatttgatcaaaaaccccacaacctgacattgaattcgactctgttcatcctcatctaaacatccgatggtctctttcatggaacagAGCTCTGCAAGATCCAGGCCGATTCAAATGAGAAGCAAACCGACTACTACTTCTTCAGTCGCAAGGACAAGAAGTATCCAACTGGCAACCGAGCCAACCG---------
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-------------------------------------------------------------------------------------------gttaaaccctaaatatgaaaaaaaactctttcattt--ctacgaactc---tctatttctttgt-tctttatttttga--accattttggtatgcaaatgcagAGGAATGTAGAA-TCGGTTCAAC---GCCACAAAACGACTGGTACTTCTTCAGCCACAAGGACAAGAAGTATCCAACCGGGACCAGGACGAACCGGGCAACAGTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|100446908|gb|CJ971207.1|CJ971207EST: TCTCATTCGCGACCTAGATCTTTACAAGCTTGAGCCGTGGGATCTTCAAG AGCTCTGCAAGATCCAGGCCGATTCAAATGAGAAGCAAACCGACTACTACT
genomic: TCTCATTCGCGACCTAGATCTTTACAAGCTTGAGCCGTGGGATCTTCAAGgtcagtacaa ... catggaacagAGCTCTGCAAGATCCAGGCCGATTCAAATGAGAAGCAAACCGACTACTACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattcgactctgttcatcctcatctaaacatccgatggtctctttcatggaacagAGCTCTGCAAGATCCAGGCCGATTCAAATGAGAAGCAAACCGACTACTACTTCTTCAGTCGCAAGGACAAGAAGTATCCAACTGGCAACCGAGCCAACCG
atctaaa putative branch site (score: 3)
tctctttcat putative PPT
atctaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtacaaactcattgcagttttttttttgtttttgtttttttaaagcaatttactcgttgaaagatatcaatagattcagaagtcagaacagagtataggatttgatcaaaaaccccacaacctgacattgaattcgactctgttcatcctcatctaaacatccgatggtctctttcatggaacagAGCTCTGCAAGATCCAGGCCGATTCAAATGAGAAGCAAACCGACTACTACTTCTTCAGTCGCAAGGACAAGAAGTATCCAACTGGCAACCGAGCCAACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT