Sequence
atgc intronic sequence ATGC exonic sequence...cctcatcatccatgatcttaagttacaaactagaattgaatccgtgagcttcctacctgttggaattctgtagtagaaagtgttaatgctttttctgtagACGGCACCGGATCGATGGCGGCTTGTGCGAGCCCATGGCCTTTCTGTAGGCCTTCCCAGCGACGAAGACATGGGAAACAGTGAGGTTGGCCACAACGCTC
Basic information
species | Physcomitrella patens |
transcript | PP1S193_45V6.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S193_45V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g21260.1 (Oryza sativa), 3'ss of exon 1
cctcatcatccatgatcttaagttacaaactagaattgaatccgtgagcttcctacctgttggaattctgtagtagaaa---gtgttaatgctttttc-----tgtagACGGCACCGGATCGATGGCGGCTTGTGCGAGCCCATGGCCTTTCTGTAGGCCTTCCCAGCGACGAAGACATGGGAAACAGTGAGGTTGGCCACAACGCTC
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-----------gtagtaacaa--cgctaacaagacgtttgtttg-atgcttccca--tgatgatcagctgagagcgagacttgtgtgtgtgttttctggcgcgtgcagGGTGGTCCGGAGAGGTGGAGGGTGATCAAGGCTCACGGGACGGCGGTGGGGCTGCCTACGGACGACGACATGGGCAACAGTGAGGTTGGCCACAACGCGC
upper sequence: PP1S193_45V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 1
cctcatcatccatgatcttaagttacaaactagaattgaatccgtgagcttcctacctgttggaattctgtagtagaaagtgttaatgct-ttttctgtagACGGCACCGGATCGATGGCGGCTTGTGCGAGCCCATGGCCTTTCTGTAGGCCTTCCCAGCGACGAAGACATGGGAAACAGTGAGGTTGGCCACAACGCTC
|| | | | | || ||| | | || || ||| | || | | ||| || | | || | | || | || | || | || || |||| || | | ||| ||||| | || || || |||||||| || ||||||||||||||||| ||||||||||| ||||
--gtatgtttcct--tttttgtttatatccacttctttcctcgatgatttcgctggattccg--attatggacttcaacggttcgattttattcttcacagGGGAAGCCCGACACATGGAGGTTGATCAAAGCTCATGGTACCGCCGTTGGTCTCCCCAGCGAAGACGACATGGGAAACAGTGAAGTTGGCCACAATGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagcttcctacctgttggaattctgtagtagaaagtgttaatgctttttctgtagACGGCACCGGATCGATGGCGGCTTGTGCGAGCCCATGGCCTTTCTGTAGGCCTTCCCAGCGACGAAGACATGGGAAACAGTGAGGTTGGCCACAACGCTC
tgttaat putative branch site (score: 3)
tgctttttct CT-rich tract
tgttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctcatcatccatgatcttaagttacaaactagaattgaatccgtgagcttcctacctgttggaattctgtagtagaaagtgttaatgctttttctgtagACGGCACCGGATCGATGGCGGCTTGTGCGAGCCCATGGCCTTTCTGTAGGCCTTCCCAGCGACGAAGACATGGGAAACAGTGAGGTTGGCCACAACGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA