Sequence
atgc intronic sequence ATGC exonic sequence...ctttaaacatttcgaacttcagaacataatatgagctaattaatttgcatcttccatctctacgtgtttttatttttatttttatttttattttgtacagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
Basic information
species | Physcomitrella patens |
transcript | PP1S40_145V6.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G156608_T04 (Zea mays), 3'ss of exon 2
------ctttaa-acatttcgaacttcagaacataatatgagctaattaatttgcatcttccatctctacgtgtttttatttttatttttatttttattttgtacagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
|| || | | |||||| | | || || ||| | || || | || || || | | | || ||||||| |||||||||||||| |||||| ||||||||||||| || || |||||||| |||| |||||||||||| ||| ||||| | ||||| ||||| || || |
agtaacctatagtgctcattgaactt---atttgattaagaaggtattcacatgaattgattaaagaaacatggttgtgacaaaaaactgatatttattt----cagGTCAGTCATCACCCAATGGTTGTTGCATGCCACTGTGACGGCAGAGGTTGGAGATTCTGGGGTGATTCCAATCTGAAAGGGAAGTTCTGGGGTCGATCCA
upper sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 6
ctttaaacatttcga-acttcag---aacataatatgagctaat-taatttgc-atcttccatctctacgtgtttttatttttatttttatttttattttgtacagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
|||| || | | || | ||| || | || | ||| ||| || | || | | | | | | |||| | || | | ||||||||||||| ||||||||||||||||||||||| ||||| | ||| |||| ||| |||||||||||||| || ||||| || |||||||| ||||| |
-----gacatatcaataatttaatttggcattattttttcttgtgtaaggtgctattgcctattcgtttgaataaaaaatacttacgctattcatcttgag-atagGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
upper sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 6
--ctttaaacatttcgaacttcagaacataatatgagctaattaatttgcatcttccatctctacgtgtttttatttttatttttatttttattttgt-acagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
| ||||||| || | | || | || | | || | || | | || | | || | | | || | || || || | ||||||||||||| || |||||||||||||||||||| ||||| || || |||| ||| |||||||||||||| || ||||| || |||||||| ||||| |
agccataaacatatcaataattt-aatttggcattatttt-ttcttgtgtaaagtg-atattgatttgaataaaaaatacttacgctattcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
upper sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA14G33410.1 (Glycine max), 3'ss of exon 5
ctttaaacatttcgaacttcagaacataatatgagctaattaatttgcatcttccatctctacgtgtttttatttt----tatttttatttttattttgt-acagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
| ||| | || | || | | || | ||| ||| | | ||||| ||||| | || ||||| | |||| | |||||||||||||||||||||||| |||||||| || || ||||| | ||| |||| ||| ||||| || |||||||| || || || |||||||| || || |
--tgaaaggcaatagaatttgaatttcaacaatggata--tgatt-atgcctttagaatatgtctgtttccattttgaaattattatatttctgttttctcacagGTCAGTCATCATCCAATGATAGTTGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGAGATAGCAACTTAAAGAGTAAATTTTGGGGTCGGTCAA
upper sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA04G43220.1 (Glycine max), 3'ss of exon 5
ctttaaacatttcgaacttcagaacataatatgagctaattaatttgcatcttccatctctac-gtgtttttatttttatttttatttttattttgta-cagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
| ||| || | | || | | | | || | || || | || || | | | | | || ||||| | ||||| || |||||||||||||| ||||||||||| ||||| || || ||||| | ||| |||| ||| |||||||| |||||| | || ||||| |||||||| || || |
--gaacacaatttggattttggtgtgaacaaaagggatatgatttggcttttttaatttatgccgcctattagaaattattaatgtttttgcttcccctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTTTGGGGGCGATCAA
upper sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA13G02610.1 (Glycine max), 3'ss of exon 7
----ctttaaacatttcgaacttcagaacataatatgagctaattaatttgcatcttccatctctacgtgtttttatttttatttttatttttattttgtacagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
| | | || ||| |||| | |||||| || | || | ||| | |||||| | || | | ||| | || | | ||||||||||||||||||||||| || ||||| || || ||||| | ||| |||| ||| ||||| || |||||||| || || || |||||||| || || |
gaaaggaaatataatttgaatttcaacattggatatgattatgccttttagaatat---gtctgtttctgttttgaaattattatatatctgctttctct-cagGTCAGTCATCATCCAATGATAGTAGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGAGATAGCAACTTAAAGAGTAAATTTTGGGGTCGGTCAA
upper sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA06G11470.1 (Glycine max), 3'ss of exon 6
ctttaaacatttcgaacttcagaacataatatgagctaattaatttgcatcttccatctcta-cgtgtttttatttttatttttatttttattttgta-cagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
| ||| || | | || | | | || || | || || | || | | | || | || ||||| | ||||| || |||||||||||||| ||||||||||| ||||| || || ||||| | ||| |||| ||| |||||||| |||||| | || ||||| || ||||| || || |
--caagacaatttggattttggtgtgaacaaaaaggatatgatttggcttttttattttatgtcgcctattagaaattattaatgtttttgcttcccctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTCTGGGGGCGATCAA
upper sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------------------ctttaaacatttcgaacttcagaacataatatgagctaattaatttgca-tcttccatc--tctacgtgtttt-tatttttatttttattttta-------ttttgtacagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
| ||| |||| ||||| | | | | | | ||| || | | || | | |||| || | | || |||| || | | || | ||||| ||||||||||||||||||||||| || || || ||||| || || |||| || |||| || || |||||| | || || ||||| |||||||
gtaactgggtttttcctttaacttttcaatcaaggttaatgggaatgagtcaaaatttacaggcaaatgcagcaacaataaactaaaatatttgttgcttcattattgtgtttt-gttgttgaatctgaaatagggcagtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
upper sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------------------------ctttaaacatttcgaactt-cagaacataatatgagctaattaat--ttgcatcttccatct-ctacgtgtttttatttttatttttatttttattttgtac-agGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
|| ||| ||| | | || | || | || | || ||| | || | || |||| | | | | |||| | |||| ||||||||||||||||||||||| || || || ||||| || || |||| || |||| || || |||||| | || || ||||| |||||||
gtaactgggtttttccttttaacttttcaatcaaggttaatgggaatgagtcaaagtttacaggcaaatgcggcaaaaaatagactaataaatttgttgcttcattcttgccttttgttattgaatctgaaaaagggcagtgatttgtgtctattgtatgctgctaattttcatctaacaagaagcttgttccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGTTGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
upper sequence: PP1S40_145V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G13170.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------ctttaaacatttcgaacttcagaac---ataatatgagctaattaatttg-catcttccatctctacgtgtttttatttttatttttatttttattttgtacagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
| || | ||||| | || || || | ||| || | ||| | || | || | | ||| || || | |||| ||||| ||||||||||| ||||||||||| |||||||| ||||| |||||||| |||||||| ||| || | ||| | || |||||||| || || |
gcaagtcaaccatcacatcattctaatgtagaagttgtattgaaaaatcatgcatgaatgtgaaaaactttaacacttcattatctttttaaatctatcagacatatataatagcaacccctcaccttctttgccaccataattctcttgttcagGTGAGTCATCATCCTATGATTGTTGCTTGCCATTGTGAGGGACAAGGGTGGAATTTCTGGGGAGACTCAAATATCAAAGGAAAATTTTGGGGACGGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatcttccatctctacgtgtttttatttttatttttatttttattttgtacagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
tttttatttttatttt CT-rich tract
atctctacgtgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttaaacatttcgaacttcagaacataatatgagctaattaatttgcatcttccatctctacgtgtttttatttttatttttatttttattttgtacagGTCAGTCATCATCCAATGATTGTTGCATGCCATTGCGAGGGCAGAGGGTGGACATTCTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG