Sequence
atgc intronic sequence ATGC exonic sequencegtgaaattcaccctttaatctatcttgacaggaaacgacaccattggtattcatatcaggagcaccctgagaattgaacttgtgcaatagtgggtgatgttttcttgcagGTATTTTGTACAAAAAGTAAGCCGAACTGCAATGCATGTCCTTTGCGCAGCGAATGCAAACACTACGCTAGCTCATATGCTAG
Basic information
species | Physcomitrella patens |
transcript | PP1S480_4V6.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S480_4V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os01g11900.1 (Oryza sativa), 3'ss of exon 8
gtgaaattcaccctttaatctatcttgacaggaaacgacaccattggtattcatatcaggagcaccctgagaattgaacttgtgcaatagtgggtgatg-ttttcttgcagGTATTTTGTACAAAAAGTAAGCCGAACTGCAATGCATGTCCTTTGCGCAGCGAATGCAAACACTACGCTAGCTCATATGCTAG
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---------------------------gtatgagacaacaactttgata---aagtgaattcaacccaattactgtgttttgatggaccatctgtgttactttccttctagGTATTTTGTACAAAAAGTAAGCCCAATTGCAACGCATGCCCAATGAGAGCTGAGTGCAAGCACTTTGCAAGTGCATTTGCCAG
upper sequence: PP1S480_4V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os05g37350.1 (Oryza sativa), 3'ss of exon 11
gtgaaattcaccctttaatctatcttgacaggaaacgacaccattggtattcatatcaggagcaccctgagaattgaacttgtgcaatagtgggtgatgttttct--tgcagGTATTTTGTACAAAAAGTAAGCCGAACTGCAATGCATGTCCTTTGCGCAGCGAATGCAAACACTACGCTAGCTCATATGCTAG
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---------gtacttca--ttagcattaaggagtttggtctcttcattagcatctaccgacgcatttgttctcttttgtttgagtaaagataaattatcataacaaatgcagGTGTTCTGTACCAAAAGCAAGCCGAATTGCAATGCATGTCCAATGAGGAGTGAATGCAGGCATTTTGCAAGTGCCTTTGCAAG
upper sequence: PP1S480_4V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os05g37410.1 (Oryza sativa), 3'ss of exon 12
gtgaaattcaccctttaatctatcttgacaggaaacgacaccattggtattcatat-caggagcaccctgagaattgaacttgtgcaatagtgggtgatgttttct--tgcagGTATTTTGTACAAAAAGTAAGCCGAACTGCAATGCATGTCCTTTGCGCAGCGAATGCAAACACTACGCTAGCTCATATGCTAG
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---------gtacttca--ttagcatctaaggagtttgttttcttcattagcatctaccgacacatttgttctcttttgtttgagtaaagataaattatcataacaaatgcagGTGTTCTGTACCAAAAGCAAGCCGAATTGCAATGCATGTCCAATGAGGAGTGAATGCAAGCATTTTGCAAGTGCCTTTGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaggagcaccctgagaattgaacttgtgcaatagtgggtgatgttttcttgcagGTATTTTGTACAAAAAGTAAGCCGAACTGCAATGCATGTCCTTTGCGCAGCGAATGCAAACACTACGCTAGCTCATATGCTAG
tgttttctt CT-rich tract
aattgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaaattcaccctttaatctatcttgacaggaaacgacaccattggtattcatatcaggagcaccctgagaattgaacttgtgcaatagtgggtgatgttttcttgcagGTATTTTGTACAAAAAGTAAGCCGAACTGCAATGCATGTCCTTTGCGCAGCGAATGCAAACACTACGCTAGCTCATATGCTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA