Sequence
atgc intronic sequence ATGC exonic sequence...attcccgcaatttcagtttcatttatttgtggaggttttcttcgtaaaactcaaaactttgacagttagtttgatatatgcatttttattcattttgcagTATGCATCGGCAACCAGAGCACGTTATGGCTTTCTTGTTGGCTGAGTTGGGGACAAGCGGGTCACTTGATGGACAGCAGCGTTTGGTTGTCAAAGGTCGA
Basic information
species | Physcomitrella patens |
transcript | PP1S81_161V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S81_161V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA02G40310.1 (Glycine max), 3'ss of exon 7
-----attcccgcaatttcagtttcatttatttgtggaggttttcttcgtaaaactcaaaactttgacagttagtttgatatatgcatttttattcattttgcagTATGCATCGGCAACCAGAGCACGTTATGGCTTTCTTGTTGGCTGAGTTGGGGACAAGCGGGTCACTTGATGGACAGCAGCGTTTGGTTGTCAAAGGTCGA
||||| | || || | | | | | || || | | | | ||| | || || || || | | || || | || ||||||||||| ||||| || || |||||||||||| | ||||| ||||| ||||| || || ||||||||||||||| | |||||||| || || |
tatgtgttcccccg-cgacatatttgtctgcatataagaaagtaattt-tacatcatatatgtttccctcttg--ttaatgtacttttacacaatc-ttatatagGATGCATCGGCAGCCAGACCATGTCATGGCTTTCTTGCTTGCTGAATTGGGTACAAGTGGCTCCCTTGATGGACAGCAGAGATTGGTTGTAAAGGGAAGG
upper sequence: PP1S81_161V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA14G38600.1 (Glycine max), 3'ss of exon 7
attcccgcaatttcagtttcatttatttgtggaggttttcttcgtaaaactcaaaactttgacagttagtttgatatatgcatttttattca-----ttttgcagTATGCATCGGCAACCAGAGCACGTTATGGCTTTCTTGTTGGCTGAGTTGGGGACAAGCGGGTCACTTGATGGACAGCAGCGTTTGGTTGTCAAAGGTCGA
| || ||| ||| ||||| || | | | | | |||| | |||| || | | | || ||| || || | || ||||||||||| ||||| || || ||||| |||||| | ||||| ||||| ||||| || || ||||||||||||||| | |||||||| || || |
----ttattaattagtttttattcctttgttgattgtatgtgttcccctatggcatatttgtcttcccttttggta-acgtacttgtatacaatcttttatatagGATGCATCGGCAGCCAGACCATGTCATGGCCTTCTTGCTTGCTGAATTGGGTACAAGTGGCTCCCTTGATGGACAGCAGAGATTGGTTGTAAAGGGAAGG
upper sequence: PP1S81_161V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv06s0004g08180.t01 (Vitis vinifera), 3'ss of exon 7
-attc---ccgcaatttcagtttcatttatttgtggaggttttcttcgtaaaactcaaaactttgacagttagtttgatatatgcatttttattcattttgcagTATGCATCGGCAACCAGAGCACGTTATGGCTTTCTTGTTGGCTGAGTTGGGGACAAGCGGGTCACTTGATGGACAGCAGCGTTTGGTTGTCAAAGGTCGA
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tgtttggatctagatgttgtttgaagttgttttcctaggaaattgttctggcaagcaaaatatcaaaatttaacctgcc-tat---ctttttcttatttttcagGATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGGGACAAGTGGATCGCTTGATGGACAGCAAAGATTAGTTGTGAAGGGAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaactcaaaactttgacagttagtttgatatatgcatttttattcattttgcagTATGCATCGGCAACCAGAGCACGTTATGGCTTTCTTGTTGGCTGAGTTGGGGACAAGCGGGTCACTTGATGGACAGCAGCGTTTGGTTGTCAAAGGTCGA
tttttattcatttt CT-rich tract
tttgatatatgcattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attcccgcaatttcagtttcatttatttgtggaggttttcttcgtaaaactcaaaactttgacagttagtttgatatatgcatttttattcattttgcagTATGCATCGGCAACCAGAGCACGTTATGGCTTTCTTGTTGGCTGAGTTGGGGACAAGCGGGTCACTTGATGGACAGCAGCGTTTGGTTGTCAAAGGTCGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA