Sequence
atgc intronic sequence ATGC exonic sequence...ctttatgattggatcattctattggagggacttttaagatgttggttccaatgggaattacagatcattctaatttggtgttgtgttcttgtttggtcagGCTTTATCTGTAGGAATATTTCCATACGTTCTTAAGCTGCTGCAAACAACAGCTACTGATTTGCGGCAGATTCTTGTGTTTATCTGGACGAAGATTTTAG
Basic information
species | Physcomitrella patens |
transcript | PP1S199_73V6.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 11
----ctttatgattggatcatt--ctattggagggact-tttaagatgttggttccaatgggaattacagatcattctaatttggtgttgtgttcttgtttggtcagGCTTTATCTGTAGGAATATTTCCATACGTTCTTAAGCTGCTGCAAACAACAGCTACTGATTTGCGGCAGATTCTTGTGTTTATCTGGACGAAGATTTTAG
||| | |||| || ||| | | | ||| | | || || | | ||| | | ||| ||| | | || || | | |||| |||||||| |||||||||||||| ||||| |||||| | ||||||||| | | || | || ||||| ||||| || || ||||| |||||| | |
gtaatttttctctcaattcatcaacttttgttgctattgttttacctatttatttataaaaggtttatgg--tgtgataacttgatacc-tatttttttatatgtagGCATTATCTGTTGGAATATTTCCATATGTTCTAAAGCTGTTACAAACAACAACACCCGAACTACGCCAGATCCTTGTATTCATATGGACAAAGATTCTTG
upper sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: AT5G01770.1 (Arabidopsis thaliana), 3'ss of exon 11
-----ctttatgattgga--tcattctattggagggacttttaagatgttggttccaatgggaa-ttacagatcattctaatttggtgttg-tgttcttgtttggtcagGCTTTATCTGTAGGAATATTTCCATACGTTCTTAAGCTGCTGCAAACAACAGCTACTGATTTGCGGCAGATTCTTGTGTTTATCTGGACGAAGATTTTAG
| ||| | || || | | || | || | || | ||| ||| | || | || | ||| ||| | || || | |||| |||||||| ||||||| ||| | ||| | |||||||||||||||||| ||| ||| | |||||||||||||| || || ||||| ||||| |||
gtacctctaatgccttgaagtcctgtttttcccttgttcttagacatttcctctcccatgttatcttgtgtgatgtccttacttgatgtgaatatttttat------agGCCTTATCTGTTGGAATATATCCTTGCGTAGTGAAGCTGCTGCAAACAACAACTATTGAGCTACGGCAGATTCTTGTTTTCATATGGACAAAGATCCTAG
upper sequence: PP1S199_73V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 11
ctttatgattggatcattctattggagggacttttaagatgttggttccaatgggaattacagatcattctaatttggtgttgtgttcttgtttggt-cagGCTTTATCTGTAGGAATATTTCCATACGTTCTTAAGCTGCTGCAAACAACAGCTACTGATTTGCGGCAGATTCTTGTGTTTATCTGGACGAAGATTTTAG
| || ||||| | || | || || || | | | | ||| ||||| | || | | ||||| | ||||| | || || |||||||||||||| ||||| |||||| ||||||||||| || | || || | || |||||||| ||||| ||||| ||||| | |
------------gtagtt--attggcatcatttccatttcatttctttttctgttcacaatatgtgattt--atttgattatggggtattgttccttgcagGCCCTGTCCGTTGGAATATTTCCATATGTTCTGAAGCTGTTGCAAACAACAACTCCAGAATTAAGACAAATTCTTGTATTTATATGGACAAAGATCCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttccaatgggaattacagatcattctaatttggtgttgtgttcttgtttggtcagGCTTTATCTGTAGGAATATTTCCATACGTTCTTAAGCTGCTGCAAACAACAGCTACTGATTTGCGGCAGATTCTTGTGTTTATCTGGACGAAGATTTTAG
ttctaat putative branch site (score: 2)
ttcttgttt putative PPT
attctaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttatgattggatcattctattggagggacttttaagatgttggttccaatgggaattacagatcattctaatttggtgttgtgttcttgtttggtcagGCTTTATCTGTAGGAATATTTCCATACGTTCTTAAGCTGCTGCAAACAACAGCTACTGATTTGCGGCAGATTCTTGTGTTTATCTGGACGAAGATTTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA