Sequence
atgc intronic sequence ATGC exonic sequence...tgtgactgtgtctgagagagggagagagagtgagttgatttaaatttattatatctagtatctactggctgatagtgttaggaatccgtggttttaccagGTACAAAAGAGAAGAATTTATGACATCACCAATGTTTTGGAAGGGATCGGGTTAATTGAAAAGAAGCTGAAAAATCGGATTAGATGGAA
Basic information
species | Physcomitrella patens |
transcript | PP1S364_42V6.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S364_42V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G09410.1 (Glycine max), 3'ss of exon 4
tgtgactgtgtctgagagagggagagagagtgagttgatttaaatttattatatctagtat-ctactggctgata-gtgttaggaatccgtggttttac-cagGTACAAAAGAGAAGAATTTATGACATCACCAATGTTTTGGAAGGGATCGGGTTAATTGAAAAGAAGCTGAAAAATCGGATTAGATGGAA
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-gtccctcttttttcttttttcaaaaaatgtta--tgaccaaaatatctgatatttattcttcctctattatatatgtatttaaatttttttcttttttatagGTGCAAAAGAGGAGAATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
upper sequence: PP1S364_42V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G35850.1 (Glycine max), 3'ss of exon 4
tgtgactgtgtctga-gagagggagagagagtgagttgatttaaatttattatatctagtatctactggctgatagtgttaggaatccgtggttttaccagGTACAAAAGAGAAGAATTTATGACATCACCAATGTTTTGGAAGGGATCGGGTTAATTGAAAAGAAGCTGAAAAATCGGATTAGATGGAA
|| || | | | | | | || | | | | ||||||| | || | ||| || ||| | | |||| |||| |||||||| || || |||||||| || |||||||||||||| || || | |||||||||||||| || || | || |||||
-gtccctcttttttccaaaatatattatgaccaaaatatctgatatttattcttcctctattatac------atgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAA
upper sequence: PP1S364_42V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA02G35850.2 (Glycine max), 3'ss of exon 5
tgtgactgtgtctga-gagagggagagagagtgagttgatttaaatttattatatctagtatctactggctgatagtgttaggaatccgtggttttaccagGTACAAAAGAGAAGAATTTATGACATCACCAATGTTTTGGAAGGGATCGGGTTAATTGAAAAGAAGCTGAAAAATCGGATTAGATGGAA-----------
|| || | | | | | | || | | | | ||||||| | || | ||| || ||| | | |||| |||| |||||||| || || |||||||| || |||||||||||||| || || | |||||||||||||| || || | || |||||
-gtccctcttttttccaaaatatattatgaccaaaatatctgatatttattcttcctctattatac------atgtatttaaaatttttccttttttatagGTGCAAAAGAGGAGGATATATGACATAACTAATGTTTTGGAAGGCATTGGTCTCATTGAAAAGAAGCTCAAGAACAGAATACATTGGAAGTACTGTGACA
upper sequence: PP1S364_42V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ05155 (Selaginella moellendorffii), 3'ss of exon 3
tgtgactgtgtctgagagagggagagagagtgagttgat-ttaaatttattatatctagtatctactggctgatagtgttaggaatccgtggttttaccagGTACAAAAGAGAAGAATTTATGACATCACCAATGTTTTGGAAGGGATCGGGTTAATTGAAAAGAAGCTGAAAAATCGGATTAGATGGAA
|| ||| || | ||| | | | | | | | ||| | | ||| | | | | ||||| |||||| |||| || ||||||||||||||||| |||||||| || || ||||| ||||||||| ||||||| |||| ||||||||
-----------------------------gtaagtgcatgctgcattcagtgtgtgtctctttcgcaacctgcttcagagaggctttcttctgcctttcagGTGCAAAAGCGAAGGATCTATGACATCACCAATGTGTTGGAAGGAATTGGCTTAATAGAAAAGAAGTTGAAAAACAGGATAAGATGGAA
upper sequence: PP1S364_42V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ05692 (Selaginella moellendorffii), 3'ss of exon 3
tgtgactgtgtctgagagagggagagagagtgagttgat-ttaaatttattatatctagtatctactggctgatagtgttaggaatccgtggttttaccagGTACAAAAGAGAAGAATTTATGACATCACCAATGTTTTGGAAGGGATCGGGTTAATTGAAAAGAAGCTGAAAAATCGGATTAGATGGAA
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-----------------------------gtaagtgcatgctgcattcagtgtctgtctctttcgcaagctgcttcagagaggctttcttctgcctttcagGTGCAAAAGCGAAGGATCTATGACATCACCAATGTGTTGGAAGGAATTGGCTTAATAGAAAAGAAGTTGAAAAACAGAATAAGATGGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttattatatctagtatctactggctgatagtgttaggaatccgtggttttaccagGTACAAAAGAGAAGAATTTATGACATCACCAATGTTTTGGAAGGGATCGGGTTAATTGAAAAGAAGCTGAAAAATCGGATTAGATGGAA
ggctgat putative branch site (score: 4)
ttttacc putative PPT
atatcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgactgtgtctgagagagggagagagagtgagttgatttaaatttattatatctagtatctactggctgatagtgttaggaatccgtggttttaccagGTACAAAAGAGAAGAATTTATGACATCACCAATGTTTTGGAAGGGATCGGGTTAATTGAAAAGAAGCTGAAAAATCGGATTAGATGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA