Sequence
atgc intronic sequence ATGC exonic sequence...ttgttgaaacatagcagagcggcctactgattttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattctctactttgatttgcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
Basic information
| species | Physcomitrella patens |
| transcript | PP1S259_67V6.1 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA15G07620.1 (Glycine max), 3'ss of exon 1
-------------------------------------------ttgttgaaacatagcagagcggcctactgattttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattctctactttgatttgcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
|| | || || | | | || | || | | | | | || || | ||| || | || | | || ||| ||| || || | |||||| || ||||||||| |||||||||||||| || ||||||||||||||||| | | |||||| ||||||| |||| || ||
gtatgcaacttcatcacaccccaacttttcttttcctcctttcatgcaaacccacttcatatttccatgcttaattgcttaccttatatttattttttggatccaatattttcatttttgactttttttgtgtttttttttagGTAAAGCAACTTTTGGTGATCAAGAGTGGTACTTTTTCAGCCCAAGGGATAGGAAATACCCAAATGGGTCAAGGCCTAACAGAGCTGCTTCTTCTGGGTA
upper sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA13G35550.1 (Glycine max), 3'ss of exon 1
ttgttgaaacatagcagagcggcctactgattttccgggaatctgtaaaagttcaagagcgtataaattaaa-agaatcgattctctactttgatttgcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
| || || || | || | || || | | | | | | | | |||||| || ||| | |||| || ||| |||||| || || ||||| || ||| ||||||||| ||||||||||| ||||||||||||||||| || || |||| || ||| ||| || | || || ||
-----gtaat-tatcaaatcg-ctcacccatctccatttttttttaagttaattactttgttctaaattgaatagatttgattgattaattt----tgcagGTAAAGCGATTTTCGGTGAAAAAGAGTGGTACTTTTTCAGCCCCAGAGACAGGAAATACCCGAACGGGTCTCGACCCAACAGAGTAGCTGGGTCGGGTTA
upper sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA12G35000.1 (Glycine max), 3'ss of exon 1
ttgttgaaacatagcagagcggcctactgattttccgggaatctgtaaaagt-tcaagagcgtataaattaaaagaatcgattctctactttgattt--gcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
| || | | | | || || | | | | | | ||| | | || | | | || |||| ||| | || |||| ||||| ||||| ||||| || || ||||||||| ||||||||||| ||||||||||||||||| || || | || || ||| ||| || | || || ||
-----gtaattcaacccactcactcacccatctccatttatttttttaaaatgttaattactttgttctgaattgaataaatttgattgattaatttttgcagGTAAGGCGATTTTCGGTGAGAAAGAGTGGTACTTTTTCAGCCCTAGAGACAGGAAATACCCTAACGGGTCCCGACCCAACAGAGTAGCCGGGTCGGGTTA
upper sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G31220.1 (Glycine max), 3'ss of exon 1
--------ttgttgaaacatagcagagcggcctactgattttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattctctactttgattt-gcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
| | |||| | | | | || | | | | |||| ||| || || ||| || || |||| | || | ||| | ||| || || | |||||| || ||||||||| |||||||||||||| || || |||||||||||||| ||| | || || ||||||| |||| || ||
caacgtgatactagaaaattcacggtgaaaccaaatacacatttgtgaatttgt-----ttt--gattgtaatgttttttcccatt--ttctttttttgggtttcgtagGTAAAGCAACTTTTGGTGAGCAAGAGTGGTACTTTTTCAGCCCAAGGGATAGAAAATACCCAAATGGGGCTAGGCCCAATAGAGCTGCTACTTCTGGGTA
upper sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA13G40250.1 (Glycine max), 3'ss of exon 1
ttgttgaaacatagcagagcggcctactgattttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattctctactttg---atttgcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
||| | | || || ||| | | | | || | | | ||| | || | || | | ||| || ||||| ||| | | |||||||| | |||||||||||| || ||||| ||||||||||| || ||||||||| | || ||| | |||||||| || |||||
--gtttgtcctttgccatgcacttcttgtgtttactaagtcttgttttgagattatagttgagaaaaatcaatctgttttttgtttttgttgtgaatgtgcagATAAGTCCTTGTTTGGAGAGGAAGAGTGGTATTTCTTTAGCCCGAGAGACAGGAAGTATCCAAATGGATTGAGGCCAAACAGGGCTGCAGCCTCAGGATA
upper sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA13G31660.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------ttgttgaaacatagcagagcggcctactgattttccgggaatctgtaaaagttcaagagc--gtataaattaaaagaatcgattctctac-tttgatttgcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
|| | | || | | || | || | || | | || || || | ||| ||| | | | | | | | ||| ||| || || | |||||| || ||| ||||| |||||||||||||| || ||||||||||||||||| | | |||||| ||||||| |||| || ||
gtatgcaacttcatcacaaaaccaccttttcttttcctcctttcatgcaaacccactttatatttttccatgactaattgcttaccttatg--aacccattgaatttttggatccaatatttattttccttttggtgtttttgtgtgttttttttagGTAAAGCAACTTTTGGTGATCAAGAATGGTACTTTTTCAGCCCAAGGGATAGGAAATACCCAAATGGGACAAGGCCTAACAGAGCTGCTACTTCTGGGTA
upper sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA06G38410.1 (Glycine max), 3'ss of exon 1
---ttgttgaaac-atagcagagcggcctactgattttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattctctactttgatttgcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
| ||| || | | | | | | | | || || | ||| ||| || || | || | | | | |||||| ||||| | |||||||| |||||||| ||||| ||||||||||||||||| ||||| ||||| | || || ||| ||| || | ||| || ||
atataattgcaattgtgatcgtgagcgtaattcaaaaccttggttaatgatattgttattagtattatgtttttaa----ttgaatgtggttatggtggtgcagGTAAGGCAGTGTTTGGAGAGAAGGAGTGGTACTTTTTTAGCCCAAGAGACAGGAAGTACCCGAATGGTTCACGACCAAACAGAGTCGCGGGTTCTGGGTA
upper sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA06G38440.1 (Glycine max), 3'ss of exon 1
-ttgttgaaa--catagcagagcggcctactgattttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattctctactttgatttgcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
| || || || |||| | || | | | | | | || | | | | | | | | | | || |||| || || ||| ||||| | | ||||||||| ||||||||||| ||||| ||||| ||||| ||||| || | || ||| | |||||| |||| || ||
gtaatttaactttatgatagagaatgaaaatggatatttagtttttttttc---tttgattttttttttctcatattttttttgtttgcatttgtttttgaagCCATGGCATCGTTTGGGGCGGAAGAGTGGTACTTTTTCAGCCCGAGAGAAAGGAAGTACCCGAATGGCGCAAGGCCAAACAGGGCTGCAACTTCAGGGTA
upper sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA12G22790.1 (Glycine max), 3'ss of exon 1
--ttgttgaaacatagca-gagcggcctactgattttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattctctac-tttgattt-gcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
| || || || | | | | || | | | | | | || | | | || | | || | | | |||||||| | || ||| || ||||| | | ||||||||| ||||||||||| ||||| ||||| ||||| ||||| || | || ||| | |||||| |||| || ||
tataatttaactttatgatgggaaatgaaatgggtatatagtattttt-----atttttattctttttctttgatttttttttttgtttgcatttgattttgaagCCAAAGCATCGTTTGGGGCGGAAGAGTGGTACTTTTTCAGCCCGAGAGAAAGGAAGTACCCGAATGGCGCGAGGCCAAACAGGGCTGCAACTTCAGGGTA
upper sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA12G29360.1 (Glycine max), 3'ss of exon 1
------ttgttgaaacatagcagagcggcctactga-ttttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattctctactttgatttgcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
||| | | | | |||| | | || || | | || | ||| | | | | || | || | | || ||||| ||| | | |||||||| | ||| |||||||| || ||||| ||||||||||| ||||| |||||| | || ||| | |||||||| || |||||
gtttgtcctttgccatgcactcgttgtgtttactaagtcttgtttgagtttataca-gttgagaaaaatgaatctttttttatgttgttgttgttgtgaatgtgcagATAAGTCCTTGTTTGGAGAGGAAGAATGGTATTTCTTTAGCCCGAGAGACAGGAAGTACCCGAATGGATTGAGGCCAAACAGGGCTGCAGCCTCAGGATA
upper sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA07G35630.1 (Glycine max), 3'ss of exon 1
ttgttgaaac-atagcagagcggcctactgattttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattct---ctactttgatttgcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
|||| | | | ||| | | ||| || || || || | || ||| | | | | | | ||| || ||||| || | ||||||||| || |||||||| || || |||||||||||||| ||||||||||| | | ||||||||||| | | || || ||
--accgaaattgcaatcgcggaccctttttaaaatcctt-aacatg-aatggtattgtattacatctcctaacacacttgttattaacttaccatggaatgcagATAAAACAGAATTTGGAGAAAATGAATGGTATTTCTTTAGTCCAAGAGACAGGAAGTACCCAAATGGGGTGAGGCCTAACCGAGCAACTGTGTCTGGGTA
upper sequence: PP1S259_67V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G52880.1 (Arabidopsis thaliana), 3'ss of exon 1
--ttgttgaaacatagcagagcggcctactgattttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattctctactttgatttg-cagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
||||||||| ||| | | | || || ||||| | || || ||| | || | | ||| | || ||| || ||| ||||||||| ||| |||||||||||||| |||||||| ||||||| || || |||||| | |||||||||||||| ||||||| ||
gtaagttgaaaca----agaccaagatcataatccgatcaga-tctgtttcatttttttttt-tactgatttttgtttttttttgtgttcttgattgtgacagCGAAAGCTTCGTTTGGAGAACAAGAATGGTATTTTTTCAGTCCAAGAGATCGGAAATATCCCAACGGAGCTAGACCTAACCGAGCTGCGACTTCCGGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaaagttcaagagcgtataaattaaaagaatcgattctctactttgatttgcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
ctttgat putative branch site (score: 5)
ttctctacttt CT-rich tract
tataaattaaaagaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgttgaaacatagcagagcggcctactgattttccgggaatctgtaaaagttcaagagcgtataaattaaaagaatcgattctctactttgatttgcagGCAAGGCTATTTTTGGAGAAGGAGAGTGGTATTTTTTCAGCCCAAGAGACAGGAAATACCCAAATGGAGCTCGCCCTAACCGAGCTGCAGCTTCCGGATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
-tgttgaa
