Sequence
atgc intronic sequence ATGC exonic sequence...tgtttattatggcacgtttgattatgttttctctttcaagacgaataggtaatacctactgccttgtgaatcagtttctaacattacattgatttcttagGGTTATTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCATGCCTACTGGGCAAAGCTGTCACTTGTAATTACTTGCGTAGAGATAATTTTCTTGAG
Basic information
species | Physcomitrella patens |
transcript | PP1S376_46V6.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S376_46V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: LOC_Os08g34060.3 (Oryza sativa), 3'ss of exon 19
-tgtttattatggcacgtttgattatgttttctctttcaagacgaataggtaatacctactgccttgtgaatcag-tttctaacattacattgatt--------tcttagGGTTATTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCATGCCTACTGGGCAAAGCTGTCACTTGTAATTACTTGCGTAGAGATAATTTTCTTGAG
| | |||| | | || || | | || |||| || | |||| | | |||| | | | ||| || | | | | | | | ||| |||||||||||||||| || ||||| ||||| |||||||| || || ||||| ||||| || || || |||||| | || ||||| ||||| |||
gtatgcattacttaatttatgtttct-tattatcttgcatg-tgaattgatttgtgaaactgg-tgataagtcaaacttttgatgtgaattgaactataaatgatctcagGGTTATTGGATGGTAAAACGTGCAGTTGGAACAAAAGCTTGTCTTCTGGGAAAAGCAGTAACATGCAATTACCTTCGCCAGGATAACTTTCTAGAG
upper sequence: PP1S376_46V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: GRMZM2G160927_T01 (Zea mays), 3'ss of exon 7
tgtttattatggcacgtttgattatgttttctctttcaagacgaataggtaatacctactgccttgtgaatcagtttctaacattacattgatttcttagGGTTATTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCATGCCTACTGGGCAAAGCTGTCACTTGTAATTACTTGCGTAGAGATAATTTTCTTGAG
|||| || || | | | | | | | | | | || || || | | | || ||| || | ||| | ||| | | |||||||||||||||| ||||||||||| || |||||||| ||||| ||||||||||| || || || ||||| | || ||||| ||||| |||
------gtatg-catgtcttagctgatgtacagtattaccatgcat--gtggta---atttgttcatg--tcaacttttg-catgaaatta---tgtcagGGTTATTGGATGGTTAAGCGTGCTGTAGGAACAAAAGCTTGCCTTCTGGGCAAAGCAGTAACGTGCAATTATCTTCGCCAGGATAACTTTCTGGAG
upper sequence: PP1S376_46V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: GLYMA15G26120.1 (Glycine max), 3'ss of exon 7
tgtttattatggcacgtttgattatgttttctctttcaagacga---ataggtaatacctact-gccttgtgaatcagtttctaac--attacattgattt--cttagGGTTATTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCATGCCTACTGGGCAAAGCTGTCACTTGTAATTACTTGCGTAGAGATAATTTTCTTGAG
||| | | || |||| || ||| | | || | |||| | || | ||| || || | ||||| ||||||||||| ||||| ||||| || |||||||| |||||||| || ||||||||||||||||| ||||| |||||||||| |||||
-----------------------gtgtgtgattctttaagatgattcatatgccttttttatttattttgtatagcattgagcaaccaatggttttcaacggatgtagGGATATTGGATGGTCAAGCGAGCTGTAGGAACAAAAGCTTGCCTACTAGGGAAAGCTGTCACTTGTAAATACTTTAAACAAGATAATTTTTTTGAG
upper sequence: PP1S376_46V6.1 (Physcomitrella patens), 3'ss of exon 18
lower sequence: AT5G35180.4 (Arabidopsis thaliana), 3'ss of exon 22
tgtttattatggcacgtttgattatgttttctctttcaagacgaataggtaatacctactgccttgtgaatcagtttctaacattacattgatttcttagGGTTATTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCATGCCTACTGGGCAAAGCTGTCACTTGTAATTACTTGCGTAGAGATAATTTTCTTGAG
|| | | | || | | | | || | | | |||| | |||| | | | | ||| | | |||| ||||||||||| ||||| |||||||| |||||||| ||| | || || |||||||| || ||||| ||| || | ||||| ||| | |||
------gtaaagaaactctgctcttctcgtttccactgaaatata---gtaaacttagtcacattgtaac-----------cgtcatggtgaat-cacagGGATATTGGATGGTCAAGCGGGCTGTTGGAACAAAAGCCTGCTTGCTCGGTAAAGCTGTGACCTGTAAGTACCTGAGGCAGGATAACTTTTTGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taggtaatacctactgccttgtgaatcagtttctaacattacattgatttcttagGGTTATTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCATGCCTACTGGGCAAAGCTGTCACTTGTAATTACTTGCGTAGAGATAATTTTCTTGAG
tttctt CT-rich tract
taacatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtttattatggcacgtttgattatgttttctctttcaagacgaataggtaatacctactgccttgtgaatcagtttctaacattacattgatttcttagGGTTATTGGATGGTGAAGCGTGCTGTTGGTACAAAAGCATGCCTACTGGGCAAAGCTGTCACTTGTAATTACTTGCGTAGAGATAATTTTCTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG