Sequence
atgc intronic sequence ATGC exonic sequence...agtaagttgtgatgagtttgttgtttttgtaaatcaggagactgagtcctgtcaatttttttataccctgcctaacatgtttttgtgtgtgattgaatagGACTGTACCTTTCCAGAGGTAATCATGAAAGTAAGAGCATGAACAAAATATATGGTTTTGAAGGAGAAGTCAACGCGAAGTTCAATGAGACTATGACGAA
Basic information
species | Physcomitrella patens |
transcript | PP1S87_139V6.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S87_139V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os05g11550.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------agtaagt--tgtgatgagtttgttgtttttgtaaatcaggagactgagtcctgtcaatt-------tttttataccctgcctaacatgtttttgtgtgtga-----ttgaat-----agGACTGTACCTTTCCAGAGGTAATCATGAAAGTAAGAGCATGAACAAAATATATGGTTTTGAAGGAGAAGTCAACGCGAAGTTCAATGAGACTATGACGAA
|||| | | || | || | | | || || || | || | | | | | |||| | ||| | | ||| | | | |||||| ||| |||||||| | ||||| || ||||| || ||||||||||| || |||||||||||||| |||||||| | ||||||| || | | | |
gtaactgctagttttgatacttttcatgaactagatattagtatgcaatctgttactttactagctcttttattacattattctaacttataatagatgtatcgattttagttgttcatgtaataaggtttcctttatacataccttgaatgatccagGTATGTACCTTGCAAGAGGAAACCATGAGAGCAAGAGCATGAATAAGATATATGGTTTTGAGGGAGAAGTGAGGTCGAAGTTGGGAGAAGCATTTATTGA
upper sequence: PP1S87_139V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G126435_T02 (Zea mays), 3'ss of exon 7
-----agtaagttgtgatgagtttgttgtttttg-taaatcaggagactgagtcctgtcaatttttttataccctgcctaacatgtttttgtgtgtgattgaatagGACTGTACCTTTCCAGAGGTAATCATGAAAGTAAGAGCATGAACAAAATATATGGTTTTGAAGGAGAAGTCAACGCGAAGTTCAATGAGAC-TATGACGAA
|||| || || | | ||||| |||| || | | ||| ||| ||| | ||| | | || | ||| | ||| || |||||||| | ||||| ||||||||||| ||||||||||||||||||||||| ||||| || ||||| | | ||| | ||||| | || ||
tacttgagcagttctggtgttatgttaacttttgataaaacatgggcttgaagt-tgtagttttactaatattgcac-tggcaaatcttttta----attttccagCTATGTACCTTGCAAGAGGAAATCATGAAAGCAAGAGCATGAACAAAATATATGGCTTTGAGGGGGAAGTGAGGTCAAAGCTGGGTGAGAAGTTTGTTGA-
upper sequence: PP1S87_139V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA08G42380.1 (Glycine max), 3'ss of exon 8
agtaagttgtgatgagtttgtt-gtttttgtaaatcaggagactgagtcctgtcaatttttttataccctgcctaacatgtttttgt-gtgtgattgaatagGACTGTACCTTTCCAGAGGTAATCATGAAAGTAAGAGCATGAACAAAATATATGGTTTTGAAGGAGAAGTCAACGCGAAGTTCAATGAGAC-TATGACGAA
| | | | | ||| | || || | |||| || || | | | || || || || ||| | ||||| || | || | ||||||| |||||||| ||||||||||||||||| |||||||||||||| || || || | ||||||| ||||| || | || |||
-ttcttctttcctcactttatccagttcggttgtttgagagaatgttattcgtttttctcctagtatattgtaacttattttgttgccatatgatttt-cagCCATATATTTAGCCAGAGGAAATCATGAGAGTAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGA-
upper sequence: PP1S87_139V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA18G12440.1 (Glycine max), 3'ss of exon 8
agtaagttgtgatgagtttgt-tgtttttgtaaatcaggagactgagtcctgtcaatttttttataccctgcctaacatgtttttgtg---tgtgattgaatagGACTGTACCTTTCCAGAGGTAATCATGAAAGTAAGAGCATGAACAAAATATATGGTTTTGAAGGAGAAGTCAACGCGAAGTTCAATGAGAC-TATGACGAA
| | | | | ||| | || || | | | |||| || ||| | | || || || |||| |||||| || ||||||| || | || | ||||||| |||||||| || |||||||||||||| |||||||||||||| || || || | ||||||| ||||| || | || ||||
--tcttctttcttcactttatctggttctcttgtttgagagaatgctatttgtttttgtcttggcacattg--taacttgttttgttgccatgtgatttt-cagcCATATATTTAGCCAGAGGAAATCATGAGAGCAAGAGCATGAACAAGATATATGGTTTTGAGGGTGAGGTGCGCTCGAAGTTGAATGAAACATTTGTCGAA
upper sequence: PP1S87_139V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: AT2G42810.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------------------------------------agtaagttgtgatgagtttgttgttt--ttgtaaatcaggagactgagtcctgtcaatttttttataccctgcc--taacatgtttttgtgtgtgattgaatagGACTGTACCTTTCCAGAGGTAATCATGAAAGTAAGAGCATGAACAAAATATATGGTTTTGAAGGAGAAGTCAACGCGAAGTTCAATGAGACTATGACGAA
| | | | | || | || ||| | | | | | | | | | || ||| || || ||| | ||| ||||| | || || | || || ||||||| || |||||||| ||||||||||||||||| ||||||||||| || || || | ||||| | ||| | | | |
gtaagttctctaaaactttgttgtaataattctttgatgttcatgttttaattgcttttgctatcactggcaaggattaaattatttactattgtctgatggggttaaaagtttccattttaattgtaaatcgccatttacacacctttgt-----actg--cagCCATATATCTAGCCAGAGGAAACCATGAAAGCAAGAGCATGAACAAAATTTATGGTTTTGAGGGTGAGGTTCGGTCCAAGTTGAGTGAAAAATTCGTGGA
upper sequence: PP1S87_139V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: Vv12s0142g00720.t01 (Vitis vinifera), 3'ss of exon 2
agtaagttgtgatgagtttgttgtttttgtaaatcaggagactgagtcctgtcaatttttttataccctgcctaacatgtttttg--tgtgtgattgaat----agGACTGTACCTTTCCAGAGGTAATCATGAAAGTAAGAGCATGAACAAAATATATGGTTTTGAAGGAGAAGTCAACGCGAAGTTCAATGAGACTATGACGAA
| || | |||||| | || | | || | || | | |||| | | |||||| || ||| || | | ||| || | || || || ||||| ||||| || || |||||||||||||| ||||||||||||||||| || |||| | ||||| | ||| || | | |
-tttgtttcctcttcctttgtt--tcatgctctctaagtaacaaaatcacaactaattttat---tctcatgtaacatcttgttgactggttcaaaaaatcttcagCTATATATCTCTCTAGAGGAAATCACGAGAGCAAGAGCATGAACAAGATATATGGTTTTGAAGGGGAGGTCAGATCCAAGTTGAGTGAAACATTTGTGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcctgtcaatttttttataccctgcctaacatgtttttgtgtgtgattgaatagGACTGTACCTTTCCAGAGGTAATCATGAAAGTAAGAGCATGAACAAAATATATGGTTTTGAAGGAGAAGTCAACGCGAAGTTCAATGAGACTATGACGAA
gcctaac putative branch site (score: 2)
tcaatttttttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtaagttgtgatgagtttgttgtttttgtaaatcaggagactgagtcctgtcaatttttttataccctgcctaacatgtttttgtgtgtgattgaatagGACTGTACCTTTCCAGAGGTAATCATGAAAGTAAGAGCATGAACAAAATATATGGTTTTGAAGGAGAAGTCAACGCGAAGTTCAATGAGACTATGACGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT