Sequence
atgc intronic sequence ATGC exonic sequencegccgatcagatggataccctcttcgactctcttcgctatccacaactacggcgacatttgcattaattctcgatgatgtttatgactgtgatgatgcattcgttggtgcagttcctaacactagagctgtttttgttttccttcttatcagGGAAGAGCTGCAGGCTGCGGTGGTTCAATCAGCTAGATCTTTGGATCAATCGTCGACCTTTCACTGAAGATGGAGAGGAGCGTCTTCTTGCTGCTCACCG
Basic information
species | Physcomitrella patens |
transcript | PP1S151_41V6.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S151_41V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ14198 (Selaginella moellendorffii), 3'ss of exon 1
gccgatcagatggataccctcttcgactctcttcgctatccacaactacggcgacatttgcattaattctcgatgatgtttatgactgtgatgatgcattcgttggtgcagttcctaacactagagctgtttttgttttccttcttatcagGGAAGAGCTGCAGGCTGCGGTGGTTCAATCAGCTAGATCTTTGGATCAATCGTCGACCTTTCACTGAAGATGGAGAGGAGCGTCTTCTTGCTGCTCACCG
| | | ||| || | || | ||| | | ||| || || || | ||| || | | | | ||||| |||| |||||||||||||||||||||||||||||||| || | |||| ||||| | || ||||| || || | |||||||| || || || || ||| |
---------------------------------------------tttctctccttgtctcatctgatcccctggagttctatcgcgat--cgatatccccggtgaccatcgtcgtctcacacga----tcatcgcgatttttctttccagGCAAGAGCTGCAGGCTGCGGTGGTTCAATCAGCTCGACCCGCGGATAAATCGGCAGCCGTTCACGGAGGAGGAGGAGGAGCGGCTGCTGGCGGCGCACAG
upper sequence: PP1S151_41V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ19990 (Selaginella moellendorffii), 3'ss of exon 1
gccgatcagatggataccctcttcgactctcttcgctatccacaactacggcgacatttgcattaattctcgatgatgtttatgactgtgatgatgcattcgttggtgcagttcctaacactagagctgtttttgttttccttcttatcagGGAAGAGCTGCAGGCTGCGGTGGTTCAATCAGCTAGATCTTTGGATCAATCGTCGACCTTTCACTGAAGATGGAGAGGAGCGTCTTCTTGCTGCTCACCG
| | | ||| || | || ||||| | | ||| || || || | ||| || | | | | ||||| |||| |||||||||||||||||||||||||||||||| || | ||||||| |||| || ||||| || || | |||||||| || || || || ||| |
---------------------------------------------tttctctccttgtctcatctgatcccctggagttttatcgcgat--cgatatccccgatgaccatcgtcgtctcacacga----tcatcgcgatttttctttccagGCAAGAGCTGCAGGCTGCGGTGGTTCAATCAGCTCGACCCGCGGATCAACCGTCAGCCGTTCACGGAGGAGGAGGAGGAGCGGCTGCTGGCGGCGCACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cattcgttggtgcagttcctaacactagagctgtttttgttttccttcttatcagGGAAGAGCTGCAGGCTGCGGTGGTTCAATCAGCTAGATCTTTGGATCAATCGTCGACCTTTCACTGAAGATGGAGAGGAGCGTCTTCTTGCTGCTCACCG
tcctaac putative branch site (score: 1)
ctgtttttgttttcct putative PPT
tttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gccgatcagatggataccctcttcgactctcttcgctatccacaactacggcgacatttgcattaattctcgatgatgtttatgactgtgatgatgcattcgttggtgcagttcctaacactagagctgtttttgttttccttcttatcagGGAAGAGCTGCAGGCTGCGGTGGTTCAATCAGCTAGATCTTTGGATCAATCGTCGACCTTTCACTGAAGATGGAGAGGAGCGTCTTCTTGCTGCTCACCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT