Sequence
atgc intronic sequence ATGC exonic sequence...gttgtattggtcaatgcttgtgaggggatctctctagcagcaaaatttcttttgtactaaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
Basic information
species | Physcomitrella patens |
transcript | PP1S96_102V6.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os09g38970.1 (Oryza sativa), 3'ss of exon 3
gttgtattggtcaatgcttgtgaggggatctc-tctagcagcaaaattt--cttttgtactaaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
| | ||| || || ||| || || || | || | |||| |||||| || || | | | || ||| | | |||| | ||||||| || | ||||||||| |||||||| || ||||||||||||||||| ||||| || |||||||||
-gtatgttgatctat-cttctggggatgcatcattcagtaaacttatttgatttttgtgttataactcttgttatacaaaat-tatttg----------gcagGTTCGCAAATTCAGTAAACACTGCAGAAGTTGTGACAAATGTGTTGATGGATTTGATCATCATTGTCGG
upper sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os08g44230.1 (Oryza sativa), 3'ss of exon 3
-----gttgtat---tggtcaatgct-----tgtgaggggatctctctagcag-------caaaat------------ttcttttgtactaaaattgtgatagtaaaaactgtgtttgtt---------------------ctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
|||||| || |||| | | || ||| | | | ||| |||||| ||| | |||| ||| |||| | || |||||| |||| | |||| ||||||| || | |||||||||||||||||| || || |||||||| ||||| ||||| || || ||||||
gtaagcttgtatatgtgctcaacgttggaactgcataatgatttttgtctcagtttcaggcaaaatatatcatttattttcctctgtaataactttgtaaaagcgaaaacttctgttgtcagatgttgctaattacaaaggcaaaattttcagGTTCGCAAATTCAGTAAACATTGCAGAAGTTGTGATAAATGTGTGGATGGTTTTGATCATCACTGTCGG
upper sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA06G01810.1 (Glycine max), 3'ss of exon 6
---gttgtattggtcaat-gcttgtgaggggatctctctagcagcaaaatttcttttgtactaaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
| | | | | || | || || | || || ||| | | | |||| |||| | | | ||| | |||| |||||||||||| |||||| ||||| |||| || ||||||||||||||||| ||||| ||||||||||||
taaaatatctagttgaagagttttctttcctttccttgcctcaccagaatatg----gaaaaaaaaccatgatgtatttacatctttttagttatattttgcagGTTCGGAAGTTCAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
upper sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA11G10180.1 (Glycine max), 3'ss of exon 3
-----gttgtattggtcaatgcttgtgaggggatctctctagcagcaaaatttcttttgtactaaaattgtg-atagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
|||| || | | || || || | | || || | | || ||| | ||| || | | ||| ||| | | ||| |||| || |||| |||||||||||| ||||| || || ||||||||||||||||| || ||||||||||||
atctggttgcat--gcagctatcagtagaggcattt-tagagaagtagcttgcgcttctcacttagtgtgtatatcttgtgcattgtattt---cctgtattgcagGTGCGCAAGTTCAGTAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
upper sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
---gttgtattggtcaatgcttgtgaggggatctctctagcagcaaaatttcttttgtactaaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
|| | | | | || || || | | || || | | | ||| | ||| ||| | | ||| | | || |||| |||| || |||| ||| |||||||| ||||| || || ||||||||||||||||| || ||||||||||||
acatttctggttgcatgagtcagtagaggcattt-tagagaagtagcttccacctctcacttagtatgt-atattctgtgccttgtatttcctgtattt-cagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
upper sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA04G01720.1 (Glycine max), 3'ss of exon 4
gttgtattggtcaatgcttgtgaggggatctctctagcagcaaaatttctttt--gtact-aaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
| || || ||| | | | ||| | | | || ||| | |||| |||| | | | ||| | |||| |||| | ||||| ||||| ||||| |||| || ||||||||||||||||| ||||| ||||||||||||
---attttaaaatatctagttgaagagttttctttcctttccttacctcaccagagtattgaaaaccatgatgtatttacatctttttaattatattttgcagGTGCAGAAGTTTAGTAAGCATTGTCGAAGTTGTGACAAATGTGTTGATGGATTTGATCACCATTGTCGG
upper sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv18s0122g00920.t01 (Vitis vinifera), 3'ss of exon 4
-gttgtattggtcaatgcttgtgaggggatctc-tctagcagcaaaatttcttttgtactaaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
|| | || | |||| | | | || | | |||| | | ||| | | || | ||| | || | | ||||||| || || | ||| |||||||||||||| || ||||||||||| ||||| ||||| || ||||||||
aatttcagtg--tggtctttgttaaaaccttgaattcagtggtcagattttggcttaaaataaagaagatcattcaagaatgttgattttgttcctctgtagGTACGCAAATTCAGCAAACATTGCAGAAGTTGTGACAAATGTGTCGATGGGTTTGATCATCATTGTCGT
upper sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
------gttgtattggtca-atgcttgtgaggggatctctctagcagcaaaatttcttttgtactaaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
||| | || | |||| | | | | | | | || |||||| || || | || || || || ||| | ||| |||| || || | ||| ||||| || ||||| || ||||||||||| ||||| ||||| ||||||||||||
actttggttatgatgtagacatgcccacatgcagcttatggtctaacaatatttccttttgggctttttttatt-taccaagaa----aatttttcatg--ttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcttttgtactaaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
tactaaa putative branch site (score: 1)
tttgttctc putative PPT
tttgtactaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgtattggtcaatgcttgtgaggggatctctctagcagcaaaatttcttttgtactaaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC