Sequence
atgc intronic sequence ATGC exonic sequencegtatgagtgtataggagcgattgcacttttggtataagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcagCCAGAGAGTGTTCGGGAGATCACTGATTTGCTGGATGCAGTTGGTAACACTACTAAAGCAACTACTAAAGGTTTTGCCATCGGCTCAGCTGCCTTAGCTT
Basic information
species | Physcomitrella patens |
transcript | PP1S105_42V6.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S105_42V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 3'ss of exon 10
gtatgagtgtataggagcgattgcacttttggtat-aagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcagCCAGAGAGTGTTCGGGAGATCACTGATTTGCTGGATGCAGTTGGTAACACTACTAAAGCAACTACTAAAGGTTTTGCCATCGGCTCAGCTGCCTTAGCTT
|| | || |||| | || || | ||| | || | |||| | || | | || | || | |||||||||||||||| || |||||||||||| | || ||||| ||||| ||||| || |||||||| || ||||| |||||||| || || ||||| | || |
------------gtaagatgtcacatgattggcttgaaaggctcttatgttc--catctttattc-----tatgtagaaataat------aaatgtttcgtgcagCCAGAGAGTGTCCGTGAGATCACTGATCTTCTTGATGCTGTTGGGAACACCACAAAAGCAACAACGAAAGGGTTTGCCATTGGATCTGCTGCACTTGCAT
upper sequence: PP1S105_42V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 11
gtatgagtgtataggagcgattgcacttttggtataagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcagCCAGAGAGTGTTCGGGAGATCACTGATTTGCTGGATGCAGTTGGTAACACTACTAAAGCAACTACTAAAGGTTTTGCCATCGGCTCAGCTGCCTTAGCTT
| | | | | | |||| || | | | |||| | ||| | || || || | |||||||||| ||||| || |||||||||||| | || ||||| ||||| || || || |||||||| || ||||| ||||| || || || |||||| | || |
--------------------gtatgagtcatgagtggttcgaattatgcctatgttgtatctttgaattttcaagcttctataaaacttatc-gtgtcttgcagCCAGAAAGTGTCCGTGAGATCACTGATGTTCTTGATGCTGTTGGGAATACCACAAAAGCAACAACAAAAGGGTTTGCTATTGGATCTGCTGCCCTTGCAT
upper sequence: PP1S105_42V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 10
gtatgagtgtataggagcgattgcacttttggtataagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctg--atttgctgtctgcagCCAGAGAGTGTTCGGGAGATCACTGATTTGCTGGATGCAGTTGGTAACACTACTAAAGCAACTACTAAAGGTTTTGCCATCGGCTCAGCTGCCTTAGCTT
| || | | | || | |||| |||| | | | || || || | | |||| || | | ||| | | |||| | | ||||| || ||||||||||||||||||||| | || ||||||||||| ||||| || ||||| || || || || || ||||| || || || || | || |
----gtagccattcta-caactgaatttttca-ataatgttggctgaatcaaaaggaact--ttagtgctttgtttt--taacttgatacaaaatgctct-tacagCCTGAAAGTGTTCGGGAGATCACTGATCTTCTTGATGCAGTTGGGAACACCACAAAAGCTACCACCAAGGGATTCGCCATTGGATCCGCGGCACTCGCATMapped 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|162189732|gb|FC366786.1|FC366786EST: TTGGACCCATTGCAGACAACGCTGGAGGCATTGTTGAAATGAGTCAACAG CCAGAGAGTGTTCGGGAGATCACTGATTTGCTGGATGCAGTTGGTAACACT
genomic: TTGGACCCATTGCAGACAACGCTGGAGGCATTGTTGAAATGAGTCAACAGgtatgagtgt ... ctgtctgcagCCAGAGAGTGTTCGGGAGATCACTGATTTGCTGGATGCAGTTGGTAACACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcagCCAGAGAGTGTTCGGGAGATCACTGATTTGCTGGATGCAGTTGGTAACACTACTAAAGCAACTACTAAAGGTTTTGCCATCGGCTCAGCTGCCTTAGCTT
tgctgat putative branch site (score: 3)
atttctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagtgtataggagcgattgcacttttggtataagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcagCCAGAGAGTGTTCGGGAGATCACTGATTTGCTGGATGCAGTTGGTAACACTACTAAAGCAACTACTAAAGGTTTTGCCATCGGCTCAGCTGCCTTAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC