Sequence
atgc intronic sequence ATGC exonic sequence...gtagcacgcattaggaaagaaatgggctcaatctgccctacatgaaaaagctctcatagatctaaatctgacacatggtgggatgtgtggactgctccagTCAGATGATCAATGCTGTAACTCATGTGAAGAGGTGCGAGAAGCATATCGCAAAAAGGGTTGGGCCTTGACCAATACGGATCTAATTGATCAG
Basic information
species | Physcomitrella patens |
transcript | PP1S15_354V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S15_354V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os03g20520.1 (Oryza sativa), 3'ss of exon 5
-------------------------------------------------------gtagc-----acgcattaggaaagaaatgggct-caat-ctgccctacatgaaaaagctctcat--agatctaaatctgacacatggtgggatgtgtggactgctccagTCAGATGATCAATGCTGTAACTCATGTGAAGAGGTGCGAGAAGCATATCGCAAAAAGGGTTGGGCCTTGACCAATACGGATCTAATTGATCAG
||| | | | ||| | | || | ||| || | || || ||| | || || | | | | | | | | | | |||||||||||||| ||||||||||| |||||||| || || || || ||||| ||||| || ||||| | ||||||| || |||||||||
gtaccttgtacacttctctaataccattatgttgagtttgcctatttttattaatgtaactatttatgtatttacacctatattatttgcaacactaatttttatccttcctcttccattgaaattgtaagaaaaactaatattgtttttattaatt-catcagTCAGATGATCAGTGCTGTAACTCCTGTGAAGACGTCCGTGATGCCTATCGGAAAAAAGGGTGGGCACTCACCAATATAGAAGAGATTGATCAG
upper sequence: PP1S15_354V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA05G24610.1 (Glycine max), 3'ss of exon 5
gtagcacgcattaggaaagaaatgggctcaatctgccctacatgaaaaagctctcatagatctaaatctg---acacatggtgggatgtgtggactgctccagTCAGATGATCAATGCTGTAACTCATGTGAAGAGGTGCGAGAAGCATATCGCAAAAAGGGTTGGGCCTTGACCAATACGGATCTAATTGATCAG
| | ||| | | | | ||| | | || | || | || | | || || | | | | | || || | ||||||||||| || || ||||| || |||||||| ||||| ||||||||| | |||||||| ||||| |||| |||| |||| | |||||||||
--actgtgtatttgtacactttcatg-tcagtgcaacttatactccaatcgtttctttatttcttatatgtctatgctttctctatcgcttgttctcatgcagTCAGATGAACACTGTTGTAATTCTTGTGAAGAAGTGCGTGAAGCATATAGGAAAAAGGGCTGGGCAATGACAAATATGGATTTGATTGATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaagctctcatagatctaaatctgacacatggtgggatgtgtggactgctccagTCAGATGATCAATGCTGTAACTCATGTGAAGAGGTGCGAGAAGCATATCGCAAAAAGGGTTGGGCCTTGACCAATACGGATCTAATTGATCAG
atctgac putative branch site (score: 3)
ctgctcc putative PPT
atctaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcacgcattaggaaagaaatgggctcaatctgccctacatgaaaaagctctcatagatctaaatctgacacatggtgggatgtgtggactgctccagTCAGATGATCAATGCTGTAACTCATGTGAAGAGGTGCGAGAAGCATATCGCAAAAAGGGTTGGGCCTTGACCAATACGGATCTAATTGATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatgg