Sequence
atgc intronic sequence ATGC exonic sequence...gttttgtgtgaggtttttggtaaggttaaaatatcaacggaattgaagtaaatagcttgttttaacaccatctaacgttgtattatccacatggtgtcagATTATATCAACTTTGAGAGGTCATTTGGATTACTCATTTGCATCAGCTTGGCACCCTGATGGACGTGTCTTTGCCACCGGAAATCAAGATACAACTTGCC
Basic information
species | Physcomitrella patens |
transcript | PP1S376_49V6.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S376_49V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G144547_T02 (Zea mays), 3'ss of exon 9
gttttgtgtgaggtttttggtaaggt-taaaatatcaacggaattgaagtaaatagcttgttttaacaccatctaacgttgtat-tatccacatggtgt-cagATTATATCAACTTTGAGAGGTCATTTGGATTACTCATTTGCATCAGCTTGGCACCCTGATGGACGTGTCTTTGCCACCGGAAATCAAGATACAACTTGCC
| ||| || |||| | | || | | | | | | ||| | | | |||| || | | || || ||| || || || | || ||||| |||||||||||||||||||| || ||||| |||||||| | || | || || || | |||||| || || |||
-gtaagtgaatggattttcttttcttctattacttttgcagggcacatggctatatcagtatgttgttggtcctaatattcaacacacacatatattgtgtagGCAATTGGCTCTCTCAGGGGTCACTTGGATTACTCATTTGCATCTGCATGGCATCCTGATGGCAATATCGTGGCAACTGGGAGTCAAGACACTACATGCA
upper sequence: PP1S376_49V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA07G40060.1 (Glycine max), 3'ss of exon 9
gttttgtgtgaggtttttggtaaggttaaaatatcaacggaattgaagtaaatagcttgttttaacaccatctaacgttgtattatccacatggtgtcagATTATATCAACTTTGAGAGGTCATTTGGATTACTCATTTGCATCAGCTTGGCACCCTGATGGACGTGTCTTTGCCACCGGAAATCAAGATACAACTTGCC
| |||| | || | |||| || || | | | || || | || | || ||| || || | | ||||| |||| | || || |||||||||||||||||||| || ||||| |||||||| ||| | ||||| || || || ||||| | ||| ||||
--gtggtgtactctgttgatttgtgttacaaattccatagg--tactgtttgcaggtaaattatgaataatttaaattttggttctttgtagACTGTCAAGC--------CTTTATGTGGACACTTGGATTACTCATTTGCATCTGCGTGGCATCCTGATGGCCGTATTTTTGCTACTGGGAACCAAGACAAAACATGCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagtaaatagcttgttttaacaccatctaacgttgtattatccacatggtgtcagATTATATCAACTTTGAGAGGTCATTTGGATTACTCATTTGCATCAGCTTGGCACCCTGATGGACGTGTCTTTGCCACCGGAAATCAAGATACAACTTGCC
atctaac putative branch site (score: 2)
ttgttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttgtgtgaggtttttggtaaggttaaaatatcaacggaattgaagtaaatagcttgttttaacaccatctaacgttgtattatccacatggtgtcagATTATATCAACTTTGAGAGGTCATTTGGATTACTCATTTGCATCAGCTTGGCACCCTGATGGACGTGTCTTTGCCACCGGAAATCAAGATACAACTTGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA