Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttcctccgccgcttcaattcattggcaattggcccattcagtaacagcattagagctcgtaagaagtatttaagattttttctctcgtgcgaaaagtgtctcatatatggctgtttgatactgacagGTCGAAGAGTGGTGGGAGCAGCCAGCATCTACTGCTGTTGATTGGATTTTAGTGGATGGACAAAATGTTGCTGCTTGGCTTGCTCATGTGAAACAACTAC
Basic information
species | Physcomitrella patens |
transcript | PP1S189_50V6.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S189_50V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA08G27740.1 (Glycine max), 3'ss of exon 9
gtaagtttcctccgccgcttcaattcattggcaattggcccattcagtaacagcattagagctcgtaagaagtatttaagattttttctctcgtgcgaaaagtgtctcatatatggctgtttgatactgacagGTCGAAGAGTGGTGGGAGCAGCCAGCATCTACTGCTGTTGATTGGATTTTAGTGGATGGACAAAATGTTGCTGCTTGGCTTGCTCATGTGAAACAACTAC
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----------------------------tcaaagttgcttaatttggtattt-cat--gatctgggtggtagacttttcacgttcctataaaatttccatt-tctattataaaatggtaacctcttctg-cagCTTGATGAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC
upper sequence: PP1S189_50V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA18G50960.1 (Glycine max), 3'ss of exon 9
gtaagtttcctccgccgcttcaattcattggcaattggcccattcagtaacagcattagagctcgtaagaagtatttaagattttttctctcgtgcgaaaagtgtctcatatatggctgtttgatactgacagGTCGAAGAGTGGTGGGAGCAGCCAGCATCTACTGCTGTTGATTGGATTTTAGTGGATGGACAAAATGTTGCTGCTTGGCTTGCTCATGTGAAACAACTAC
| | | |||| |||| || | || | ||| | || | || || || | | || ||||| | | ||| ||| | | | || | ||||| ||||||||||||||||||||||| || | |||||| ||| | ||||||||| |||||||| |||| |||| | |||||||||||| || |
-----tcctcaaagttgctt-aatt---tgatatttcatctggctggtag-atttttcacgttcctataaaatttcta------tttctattatt---aaattgtaacctcttctgcagCTTGAT--------------GAGTGGTGGGAGCAGCCAGCATCGACAGTTGTTGACTGGGTAACAGTGGATGGGCAAAATGTAACTGCCTGGCATAATCATGTGAAACAGCTTC
upper sequence: PP1S189_50V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv14s0083g00990.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtttcctccgccgcttcaattcattggcaattggcccattcagtaacagcattagagctcgtaagaagtatttaagattttttctctcgtgcgaaaagtgtctcatatatggctgtttgatactgacagGTCGAAGAGTGGTGGGAGCAGCCAGCATCTACTGCTGTTGATTGGATTTTAGTGGATGGACAAAATGTTGCTGCTTGGCTTGCTCATGTGAAACAACTAC
| | | | | | || || | | | ||||| | ||| | | | | || | | || | || | | |||||| ||| | || |||||||||||||| |||||||| || | |||||| ||| || ||| ||||| ||||||||||||||||||| | ||| ||||| || || |
--------------------------actag--acttacattagcattatggatacgtagttctatttaagttatttggtttatttccatttg-gttttaaaccttttatttttgacatt---atactg-cagCTTGATGAGTGGTGGGAGCAACCAGCATCAACCGTTGTTGACTGGGTTACAGTTGATGGGCAAAATGTTGCTGCTTGGCATAATCACGTGAAGCAGCTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agattttttctctcgtgcgaaaagtgtctcatatatggctgtttgatactgacagGTCGAAGAGTGGTGGGAGCAGCCAGCATCTACTGCTGTTGATTGGATTTTAGTGGATGGACAAAATGTTGCTGCTTGGCTTGCTCATGTGAAACAACTAC
gtttgat putative branch site (score: 5)
tcatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttcctccgccgcttcaattcattggcaattggcccattcagtaacagcattagagctcgtaagaagtatttaagattttttctctcgtgcgaaaagtgtctcatatatggctgtttgatactgacagGTCGAAGAGTGGTGGGAGCAGCCAGCATCTACTGCTGTTGATTGGATTTTAGTGGATGGACAAAATGTTGCTGCTTGGCTTGCTCATGTGAAACAACTAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT