Sequence
atgc intronic sequence ATGC exonic sequence...atttttaaacgtttcagagaaaagtcttcgaggttgagtatgctgagtgatttcactttcacgtgtgcgaaataatttgaagttgcatgatgatatgcagGTGGCGAAGGAGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGG
Basic information
species | Physcomitrella patens |
transcript | PP1S78_99V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S78_99V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA03G33240.1 (Glycine max), 3'ss of exon 5
atttttaaacgtttcagagaaaagtcttcgaggttgagtatgctgagtgatttcact--ttcacgtgtgcgaaataatttgaa--gttgcatgatgat---atgcagGTGGCGAAGGAGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGG
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------actgattattgtaactagttatagat-taaagaacactaattaatattgttattttattcttggcaactcatctcttttatcttatgctaatctaatgtagGTGGCAAAGGAAGCTTCAGATATGGTGTTGGCAGATGATAATTTTAGTTCAATTGTTGCTGCTGTTGGTGAGGGTAGATCTATCTACAATAATATGAAGG
upper sequence: PP1S78_99V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA19G35960.1 (Glycine max), 3'ss of exon 5
atttttaaacgtttcagagaaaagtcttcgaggttgagtatgctgagtgatttcactttcacgtgtgcgaaataatttgaagttgcatgatgata-tgcagGTGGCGAAGGAGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGG
| | | || | | || ||| || | || | | || | | | ||| | || || | || ||||||| ||||| || |||| |||||| | ||||||||||||||||| | ||||| || |||||||| || ||| | || || ||||||||||||||||
-tgactgattattgtaattagttagattaaaggacactaattaatattgttattttgtttttggcaactcatctcttttatcttatgctattccaatgtagGTGGCAAAGGAAGCTTCAGATATGGTGTTGGCAGATGATAATTTTAGTTCAATTGTTGCTGCTGTTGGTGAGGGTAGATCTATCTACAATAATATGAAGG
upper sequence: PP1S78_99V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G07670.1 (Arabidopsis thaliana), 3'ss of exon 6
atttttaaacgtttcagagaaaagtcttcgaggttgagtatgctgagtgatttcactttcacgtgtgcgaaataatttgaagttgcatgatgatatgcagGTGGCGAAGGAGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGG
|| ||||| | || ||| | | ||||| | | | | | | ||| | | || | | ||||| || ||||||||| | ||| ||||| | |||||||||||||| ||||| ||||| ||||||||||| ||||| | || || || || || |||||||
----gtagttgtttctc-------ttctcccttctgaaaggacgggatgattatagctctatcagctt-------tctaaagct-cttggaatttttcagGTAGCAAAGGAGGCATCTGACTTGGTGTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTTGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
upper sequence: PP1S78_99V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G07810.1 (Arabidopsis thaliana), 3'ss of exon 6
atttttaaacgtttcagagaaaagtcttcgaggttgagtatgctgagtgatttcactttcacgtgtgcgaaataatttgaagttgcatgatgatatgcagGTGGCGAAGGAGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGG
| | | ||| | || | || | | |||| | | | | | | ||| | | | ||||||| || ||||||||| | |||||||| | |||||||||||||| ||||| ||||| |||||||| || ||||| | || || || || || |||||||
-----------gtactgtttctcttctctcatcttca--attccggatgatgatagctctatcagctt-------tctaaagctctg-ggcattttgcagGTAGCAAAGGAGGCATCTGACATGGTTTTGGCAGATGATAATTTCAGCACCATTGTTGCAGCTGTAGGTGAAGGCAGGTCCATCTATAACAACATGAAGG
upper sequence: PP1S78_99V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ25083 (Selaginella moellendorffii), 3'ss of exon 5
atttttaaacgtttcagagaaaagtcttcgaggttgagtatgctgagtg-atttcactttcacgtgtgcgaaataatttgaagttgcatgatgatatgcagGTGGCGAAGGAGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGG
||||||| | ||| |||||| | |||| | || | | | | | ||||||| || |||||||| ||||||||||| || || || ||||| || |||||||||||| || |||| ||||| | ||||| |||| || ||||| |
-------------------------------------gtatgcttttttcattgggttttcac-tttgcggtaagatctaactctactt-------tgcagGTTGCCAAGGAGGCCGCAGACATGGTTCTCGCTGACGATAACTTCAGCACGATTGTGAGTGCCGTTGCCGAAGGAAGATCGATTTACAGCAACATGAAAG
upper sequence: PP1S78_99V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ35276 (Selaginella moellendorffii), 3'ss of exon 5
atttttaaacgtttcagagaaaagtcttcgaggttgagtatgctgagtgatttcactttcacgtgtgcgaaataatttgaagttgcatgatgatatgcagGTGGCGAAGGAGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGG
| | | ||| | || | | || ||| |||| || | ||||| || || || || |||||||||||| | ||||| ||||| || ||||||||||| |||| |||| |||||||||||| || ||||| || ||||| |
-----------------------------------------gtacaaaaaaatcattatcg-gaacgttctatgtactga--ctgca--atc-cacacagGTAGCAAAAGAAGCTGCAGACATGGTGTTGGCAGACGATAACTTCAGCACGATTGTATCAGCCGTTGCAGAAGGTCGTTCAATCTACAACAACATGAAAG
upper sequence: PP1S78_99V6.2 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ29960 (Selaginella moellendorffii), 3'ss of exon 5
atttttaaacgtttcagagaaaagtcttcgaggttgagtatgctgagtgatttcactttcacgtgtgcgaaataatttgaagttgcatgatgatatgcagGTGGCGAAGGAGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGG
|| | | | | | || ||| | | | | | | | | | | | | ||||||| || |||||||| ||||||||||| || || || ||||| || |||||||||||| || |||| ||||| | ||||| |||| || ||||| |
--------------------------------gtatacttttttcattggtttttcactggt-ttttcactttgcggtaagatctaactctactttgcagGTTGCCAAGGAGGCCGCAGACATGGTTCTCGCTGACGATAACTTCAGCACGATTGTGAGTGCCGTTGCCGAAGGAAGATCGATTTACAGCAACATGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgatttcactttcacgtgtgcgaaataatttgaagttgcatgatgatatgcagGTGGCGAAGGAGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGG
aaataatttgaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttttaaacgtttcagagaaaagtcttcgaggttgagtatgctgagtgatttcactttcacgtgtgcgaaataatttgaagttgcatgatgatatgcagGTGGCGAAGGAGGCAGCAGACATGGTGCTTGCAGATGATAATTTTAGCACGATTGTGGCAGCTGTTGGAGAAGGTCGTTCGATATACAATAATATGAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA