Sequence
atgc intronic sequence ATGC exonic sequenceGACTATGGGCATGCTCAGTACTGCGGGCTATGTGTTGACGATGGACATGTTTGGACCCATTGCAGACAACGCTGGAGGCATTGTTGAAATGAGTCAACAGgtatgagtgtataggagcgattgcacttttggtataagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcag
Basic information
species | Physcomitrella patens |
transcript | PP1S105_42V6.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S105_42V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G069410_T01 (Zea mays), 5'ss of exon 2
GACTATGGGCATGCTCAGTACTGCGGGCTATGTGTTGACGATGGACATGTTTGGACCCATTGCAGACAACGCTGGAGGCATTGTTGAAATGAGTCAACAGgtatga-----gtgtataggagcgattgcacttttggtataagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcag
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AACAATGGGGATGCTTAGCACTGCAGGGTATGTTCTCACCATGGACATGTTTGGTCCTATAGCTGACAACGCTGGTGGTATTGTTGAGATGAGCCAGCAGgtatggcacatgtttcttttatagctcaaacctccgctgta--gcctataggttgtagcaaa-caacctgtattatt-taatactctttccattacaagatctc-----
upper sequence: PP1S105_42V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 5'ss of exon 10
GACTATGGGCATGCTCAGTACTGCGGGCTATGTGTTGACGATGGACATGTTTGGACCCATTGCAGACAACGCTGGAGGCATTGTTGAAATGAGTCAACAGgtatgagtgtataggagcgattgcacttttggtataagggtagtaatgcttaatattt-ctatttggagttttgcattgctgatttgctgatttgctgtctgcag
|| ||||| ||||| || ||||| | ||||| | || |||||||||||||| ||||| || ||||||||||| || ||||| || ||||| || |||||| || | | || || | | || || | ||| | || ||| | | || || | || || || | |
TACAATGGGAATGCTAAGCACTGCAGCTTATGTCCTTACTATGGACATGTTTGGCCCCATAGCTGACAACGCTGGTGGGATTGTCGAGATGAGCCAGCAGgtaagatgtcacatga-----------ttggcttgaaaggctcttatgttccatctttattctatgtagaaata-ataaatgtttcgtgcag-------------
upper sequence: PP1S105_42V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: EFJ13082 (Selaginella moellendorffii), 5'ss of exon 9
GACTATGGGCATGCTCAGTACTGCGGGCTATGTGTTGACGATGGACATGTTTGGACCCATTGCAGACAACGCTGGAGGCATTGTTGAAATGAGTCAACAGgtatgagtgtataggagcgattgcacttttggtataagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcag
|| ||||| ||||| ||||| || | || |||||||| |||||||||||||| |||||||| || || ||||| || |||||||| ||||| ||||| ||| | | | | | | ||| | | || |||
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGTTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaatttcgtgtt-ctatgttttgaactggaatttggttttgcag-----------------------------------------------------
upper sequence: PP1S105_42V6.1 (Physcomitrella patens), 5'ss of exon 11
lower sequence: EFJ14101 (Selaginella moellendorffii), 5'ss of exon 9
GACTATGGGCATGCTCAGTACTGCGGGCTATGTGTTGACGATGGACATGTTTGGACCCATTGCAGACAACGCTGGAGGCATTGTTGAAATGAGTCAACAGgtatgagtgtataggagcgattgcacttttggtataagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcag
|| ||||| ||||| ||||| || | || ||| |||| |||||||||||||| |||||||| || || ||||| || |||||||| ||||| ||||| ||| | | | | | | |||| | | || |||
TACAATGGGGATGCTGAGTACAGCTGCGTACGTGCTGACCATGGACATGTTTGGTCCCATTGCTGATAATGCTGGCGGAATTGTTGAGATGAGCCAACAAgtaagtgcaatttcgtgtt-ctatgtttttaactggaatttggtt-tgcag-----------------------------------------------------Mapped 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
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GACTATGGGCATGCTCAGTACTGCGGGCTATGTGTTGACGATGGACATGTTTGGACCCATTGCAGACAACGCTGGAGGCATTGTTGAAATGAGTCAACAGgtatgagtgtataggagcgattgcacttttggtataagggtagtaatgcttaatatttctatttggagttttgcattgctgatttgctgatttgctgtctgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG