Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttcgtttacccccccttcttacttcgcttttgtgtgattatatttgatatcccagcagaggctgagagatttgtaagcatggtctgtgtgatacgtatctcggattgtagtgtgctaaattatgtttgcaacatatcgtgcagGGAGTGGTACTCTTGGCATTTCCCCGAGCTGGTGAAGATTGTGAATGACAACTACACATATGCCAAGCTAGTTAAGTTTGTGAAGGACAAATCGAGCCTC
Basic information
species | Physcomitrella patens |
transcript | PP1S88_119V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S88_119V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 3
gtgagtttcgtttacccccccttcttacttcgcttttgtgtgattatatttgatatcccagcagaggctgagagatttgtaagcatggtctgtgtgatacgtatctcggattgtagtgtgctaaattatgtttgcaacatatcgtgcagGGAGTGGTACTCTTGGCATTTCCCCGAGCTGGTGAAGATTGTGAATGACAACTACACATATGCCAAGCTAGTTAAGTTTGTGAAGGACAAATCGAGCCTC
|||| ||| | | | || || | | ||| || | |||||| |||| | ||| ||| |||||| || ||| | |||||||| ||||| ||||||||||| || |||||||| || || |||||||| |||||| ||| | ||| | | ||||||||| | ||||||| |
------------------------------------aacaaacttatttttaccaattctgttgacgc-aatacgtttaaaa---tactctgtgcgatattggtatcga-------tgtaataaattg-gtgcttaac-cacaatgcagGGAATGGTATTCTTGGCATTTTCCTGAGCTGGTCAAAATCGTGAATGATAACTACGTTTATTCTAAGATTGCAAAGTTTGTGGTGAACAAATCTGATTTA
upper sequence: PP1S88_119V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G110233_T01 (Zea mays), 3'ss of exon 3
--gtgagtttcgtttacccccccttcttact--tcgcttttgtgtgattata--tttgatatcccag---cagaggctgagagatttgtaagcatggtctgtgtgatacgtatctcggattgt-----agtgtgctaa---attatgtttgcaacatatcgt-gcagGGAGTGGTACTCTTGGCATTTCCCCGAGCTGGTGAAGATTGTGAATGACAACTACACATATGCCAAGCTAGTTAAGTTTGTGAAGGACAAATCGAGCCTC
| ||| | | | | | | | | || | ||||| | ||| || | || | | | | || || | |||| | ||| | || | | | | | | || | | ||| || ||| | | | | ||||||| |||| ||| ||||| ||||| ||||| || ||||||||||||||||| ||| ||||||||||| | ||||||| | | ||||||| |
gtactgtccttgttcatgttctcatataattgtttatggttaacttcttataagcgtaataggccgtatttatagacagtctgctctgatagaaaactctg-ataatatgaatatgcaaatattccttattatgattatttattgctttctcaataaaacattgcagGGAATGGTTCTCATGGCACTTCCCTGAGCTTGTCAAGATTGTGAATGACAATTACCTTTATGCCAAGCTTGCTAAGTTTATTGTGAACAAATCTGATTTG
upper sequence: PP1S88_119V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G144995_T01 (Zea mays), 3'ss of exon 3
gtgagtttcgtttacccccccttcttacttcgcttttgtgtgattatatttgatatcccagcagaggctgagagatttgtaagcatggtctgtgtgatacgtatctcggattgtagtgtgctaaattatgtttgcaacatatcgtgcagGGAGTGGTACTCTTGGCATTTCCCCGAGCTGGTGAAGATTGTGAATGACAACTACACATATGCCAAGCTAGTTAAGTTTGTGAAGGACAAATCGAGCCTC
|| | | |||| | || || || || || | || || |||| | ||| |||| ||| ||| | | | || | | | || || | | |||| |||||||| |||| ||| ||||| ||||| ||||| || ||||||||||| ||||| ||| |||||||||||| | ||||||| | | ||||||| |
---------gtctgttgcttgttctcctataactgtttattgtcaattttctaagaggcatcataggcagggagctttgaggatatgaatgtgccaatatgcccttggtatgattatttactgttttctcaataaaacac----tgcagGGAATGGTTCTCATGGCACTTCCCTGAGCTTGTCAAGATTGTGAACGACAATTACCTATATGCCAAGCTTGCTAAGTTTATCGTGAACAAATCTGATTTG
upper sequence: PP1S88_119V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 3
gtgagtttcgtttacccccccttcttacttcgcttttgtgtgattatatttgatatcccagcagaggctgagagatttgtaagcatggtctgtgtgatacgtatctcggattgtagtgtgctaaattatgtttgcaacatatcgtgcagGGAGTGGTACTCTTGGCATTTCCCCGAGCTGGTGAAGATTGTGAATGACAACTACACATATGCCAAGCTAGTTAAGTTTGTGAAGGACAAATCGAGCCTC
| || | | | || | | | | | || | || |||| | || | | || |||| | ||| ||||| | | || | | | ||| || |||| | ||| |||||| |||||||| ||||||||||| || ||||||||||| ||||| ||||| || || |||||||| | | || ||| | |||| || | | |
------gtagtatgtctcaaatt-tgaatgctcaatta-attatagaattttcttattcaatataatttgttttctttgagaacat------tgtgaactgga----agaattcatttctcta--tttgctttgtcaattat-gtgcagAGAGTGGTATTCTTGGCATTTTCCTGAGCTGGTGAAAATTGTAAATGATAATTATCTGTATGCCAAAGTTGCAAAATTTATTGAGGATAAGGCAAAGTTG
upper sequence: PP1S88_119V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtttcgtttacccccccttcttacttcgcttttgtgtgattatatttgatatcccagcagaggctgagagatttgtaagcatggtctgtgtgatacgtatctcggattgtagtgtgctaaattatgtttgcaacatatcgtgcagGGAGTGGTACTCTTGGCATTTCCCCGAGCTGGTGAAGATTGTGAATGACAACTACACATATGCCAAGCTAGTTAAGTTTGTGAAGGACAAATCGAGCCTC
| | | | ||| | |||||| | || | | | || ||| || | |||| || | | | |||||| ||||| || ||||| |||||||| || |||||||| || ||||||||||| || ||| | ||| | | | ||||| || | |
--------------------------------------------------------------gtttgttttgtgcttttccctttcagattgtgtgttttcc-tcgagaaaattggta-gctgaact--gtttataatgt-tattacagGGAATGGTATTCGTGGCACTTCCCCGAACTAGTGAAGATAGTCAATGACAACTATCTTTACGCCCGTGTTTCAAAGATGATTGATGACAAGTCAAAGTTG
upper sequence: PP1S88_119V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 3
gtgagtttcgtttacccccccttcttacttcgcttttgtgtgattatatttgatatcccagcagaggctgagagatttgtaagcatggtctgtgtgatacgtatctcggattgtagtgtgctaaattatgtttgcaacatatcgtgcagGGAGTGGTACTCTTGGCATTTCCCCGAGCTGGTGAAGATTGTGAATGACAACTACACATATGCCAAGCTAGTTAAGTTTGTGAAGGACAAATCGAGCCTC
| | | | || | | | ||| || | || | | | | | | || | || || || |||| | |||||||| |||||||||||||||||||| ||| |||||||||| |||||||||||||| |||||||| | | || ||||| || |||| | | |
----------------------------------------taaactggagtaaaattctggtttccaaatgggagtttctag---ttgttttcctatttcttcttgttgact------tggtagttttcatttgattttcaatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatacgtatctcggattgtagtgtgctaaattatgtttgcaacatatcgtgcagGGAGTGGTACTCTTGGCATTTCCCCGAGCTGGTGAAGATTGTGAATGACAACTACACATATGCCAAGCTAGTTAAGTTTGTGAAGGACAAATCGAGCCTC
tgctaaa putative branch site (score: 2)
taaattatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttcgtttacccccccttcttacttcgcttttgtgtgattatatttgatatcccagcagaggctgagagatttgtaagcatggtctgtgtgatacgtatctcggattgtagtgtgctaaattatgtttgcaacatatcgtgcagGGAGTGGTACTCTTGGCATTTCCCCGAGCTGGTGAAGATTGTGAATGACAACTACACATATGCCAAGCTAGTTAAGTTTGTGAAGGACAAATCGAGCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT