Sequence
atgc intronic sequence ATGC exonic sequence...ttattctaacatgtgatgcttgtagattcttattttattttggtttaggtattttatttttctcataggccattaatatatttggttttgtgatgaatagATACCAAGAAGGTTCAAAAGCAAAGTTGAAGGAAAAATGGGATATGAGGATTTTGTGTGGTTTATATTATCAGAAGAAGATAAAACATCTGAGACTAGCC
Basic information
species | Physcomitrella patens |
transcript | PP1S191_94V6.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G148323_T01 (Zea mays), 3'ss of exon 8
-ttattctaacatgtgatgcttgtagattcttattttattttggtttaggtattttatttttctcataggccattaatatatttggttttgtgatgaatagATACCAAGAAGGTTCAAAAGCAAAGTTGAAGGAAAAATGGGATATGAGGATTTTGTGTGGTTTATATTATCAGAAGAAGATAAAACATCTGAGACTAGCC
||| |||| | | | | |||| || | | | || | ||| | | ||| ||| |||| ||||| ||||| | |||| ||||| |||||||| ||||| ||||| || ||||| | |||||||||||||| ||||| ||| |||||||| |||| |
gttagtctactcaattttagcatcaaaaccttagccctttattaccaaaatgttgtgctttgt------gtcctta-tattggcccttttactgcttttagATCCCAAGGAAATTCACAAGCATGACAGAAGGAAAGATGGGTTATGAAGACTTTGTTTACTTTATATTATCAGAGGAAGACAAATCATCTGAGCCTAGTC
upper sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA10G30930.1 (Glycine max), 3'ss of exon 8
------------------------------------------------------------------------------ttattctaacatgtgatgcttgtagattcttat---tttattttggtttaggtattttatttttctcataggccattaatatatttggttttgtgatgaat-agATACCAAGAAGGTTCAAAAGCAAAGTTGAAGGAAAAATGGGATATGAGGATTTTGTGTGGTTTATATTATCAGAAGAAGATAAAACATCTGAGACTAGCC
| ||||||| || | | | | | | | || ||||| |||| | ||| | | | || | | | ||| ||| | || | || | |||||| ||| | ||||| ||||| ||||| ||||||||||| |||||||| | || ||| |||||||||| |||||| ||||||| | || |
gtttgtgtggattacttgttgcttctgtctttgagatttaactgtttctgacttcagcaacagaccctataccccttttctttctaacgcaagaagtgtttggttcagtgtccattcatttttttttatcagatcattttatagaagatgcagattctg-acttgctttattattgtctcagGTCACAAGAAAGTTTACCAGCAAGGTTGAGGGAAAGATGGGATATGAAGATTTTGTTTACTTCATACTATCAGAAGAGGATAAATCATCTGAACCAAGTC
upper sequence: PP1S191_94V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv14s0036g00750.t01 (Vitis vinifera), 3'ss of exon 5
--ttat-tctaacatgtgatg-------cttgtagatt--cttattttattttggtttaggt--attttatttttctca-taggccattaatatatttggttttgtgatgaatagATACCAAGAAGGTTCAAAAGCAAAGTTGAAGGAAAAATGGGATATGAGGATTTTGTGTGGTTTATATTATCAGAAGAAGATAAAACATCTGAGACTAGCC
|| | ||| || | || || ||||| | | | |||| ||| |||| | || | | | ||| | | | || || |||| ||||||| ||| | ||||| |||||||| || ||||||||||| |||||||| | || ||| | || ||||| ||||||||||||||| |||| |
gtttgtgtctgtcagataataaattcgttttttagatcaaatgagctgctttttacggaggagaatttcacattcgtgaatgcttcatctcttagtatttcttcgtttctctcagATTCCAAGAAAGTTTACGAGCAAGGTTGAAGGCAAGATGGGATATGAAGATTTTGTCTACTTCATACTGTCGGAAGAGGATAAAACATCTGAGCCTAGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taggtattttatttttctcataggccattaatatatttggttttgtgatgaatagATACCAAGAAGGTTCAAAAGCAAAGTTGAAGGAAAAATGGGATATGAGGATTTTGTGTGGTTTATATTATCAGAAGAAGATAAAACATCTGAGACTAGCC
cattaat putative branch site (score: 3)
attaatatatttggtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttattctaacatgtgatgcttgtagattcttattttattttggtttaggtattttatttttctcataggccattaatatatttggttttgtgatgaatagATACCAAGAAGGTTCAAAAGCAAAGTTGAAGGAAAAATGGGATATGAGGATTTTGTGTGGTTTATATTATCAGAAGAAGATAAAACATCTGAGACTAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG