Sequence
atgc intronic sequence ATGC exonic sequencegtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
Basic information
species | Physcomitrella patens |
transcript | PP1S18_231V6.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os12g18770.1 (Oryza sativa), 3'ss of exon 5
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttca-----tctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
| ||||| | |||| | || ||| ||| | | || | | || | | | ||| | | || | | ||| || || || | | | | ||| |||||| || ||||| |||||| |||| ||||||||||| || || ||||| ||||| |||||||| || || ||||| | ||||| ||||| || || |
---------------------------------------------------------------------gttgtgtagtt--atttgagagcatggaga-attattccttactaaattatttcctaattctgaatgcttttcttagtgttgtgtaatttttttgagaaacatgttcttattgtgtgttaacgtgtctttcagGTCAGTCATCACCCAATGGTTGTTGCATGTCACTGTGAAGGAAGAGGTTGGAAGTTTTGGGGGGATTCAAATCTGAAAGGGAAGTTCTGGGGTCGATCAA
upper sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 5
---------------gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaatt-ttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
|||| ||| | | |||| | | | ||| || |||| | | ||| |||| || |||| | ||| | | | || || | || | | | || || || ||| | |||| | ||| || || | ||||||| | | || || | |||| || |||||||| ||| | ||||||||||||| ||||| | ||| |||||||||||||| |||||||| |||| ||||| || ||||| | || |
gtcagtttggcacccaacacatataagtttagct---aattatcaattattgtttggtcacttaacaaatcattctgaatataggcctgaaagaggaatcactaaaaacatcacgtacaaggatccaccactggagtat----tactaaaattttattatatatgagaacacacttga-ctaaatgtttttgtttat-tcttgcacc----agGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTGAAGAGCAAATTCTGGGGACAATCCA
upper sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G409265_T01 (Zea mays), 3'ss of exon 5
----gtgtgatatggtttttgttttcaattgtatgatgctt-ttttgtgtcttatggacctgtcgcatctattagccttgtagctgaatt-ttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
|| || ||| | | || || || ||| || |||| || | ||| |||| || |||| | | | | | | | || | | | | | ||| || | | | | |||| | ||| || || | || ||| | || || | |||| || |||||||| ||| | ||||||||||||| ||||| | ||| |||||||||||||| |||||||| | || ||||| || ||||| | || |
gtcagtttggtatccaccacataaattaatgctcaattattgtttagtcacttaacagactatactgaatataggcctgaaagaggaatcactaagagcatcacgtacatgaatacagcaatggagtat-tattactaaagttctattatatatgagaacacacctga-ctaaatgtgcttatttattcttggcacc----agGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTAAAGAGCAAATTCTGGGGACAATCCA
upper sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA04G43220.1 (Glycine max), 3'ss of exon 5
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
| | ||||| || | | | ||| | | | || | || ||| |||| | | || | ||||| || ||||||| || | ||||||| || ||||| ||||||||||| ||||||||||| ||||| | ||| ||||||||||||||||| |||||| | || ||||| |||||||| || || |
---------------------------------------------------------------------------gaacacaatttgga----ttttggtgtgaacaaaagggatatgatttggcttttttaa----tttatgcc--gcctattagaaattattaa--------tgtttttgcttccc----ctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTTTGGGGGCGATCAA
upper sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 6
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
|| || | | | ||| | || | || | | | |||| | | | || || | ||| | || | ||| |||| || | |||| || ||||| ||||||||||| ||||| || || ||||| | ||||||||||||||||||||||||||| || ||||| || |||||||| ||||| |
---------------------------------------------------------------------------------------gacatatcaataatttaatttgg---cattattttt-tcttgtgtaaggtgctattgcctattcgtttgaataaa----aaatactta--cgctattcatcttgagatagGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
upper sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA13G02610.1 (Glycine max), 3'ss of exon 7
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttagg-tccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
|||| | | || | | | || | | | | | |||| |||||| | | ||| | || | |||| || || | ||| | |||||||||| || |||||||||||||| || ||||||||||| ||||| | ||| |||||||||||||| || |||||||| || || || |||||||| || || |
---------------------------------------------------------------------------------------gaaa---ggaaatat-aatttgaatttcaacattggatatgattatgccttttagaatatgtctgtttc----tgttttgaaattatta---tatatctgctttctctcagGTCAGTCATCATCCAATGATAGTAGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGAGATAGCAACTTAAAGAGTAAATTTTGGGGTCGGTCAA
upper sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G11470.1 (Glycine max), 3'ss of exon 6
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
| ||||| || | | | ||| | | || | || ||| ||||| ||| || | ||||| || ||||||| || | ||||||| || ||||| ||||||||||| ||||||||||| ||||| | ||| ||||||||||||||||| |||||| | || ||||| || ||||| || || |
---------------------------------------------------------------------------caagacaatttgga----ttttggtgtgaacaaaaaggatatgatttggctttttta----ttttatgtc--gcctattagaaattattaa--------tgtttttgcttccc----ctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTCTGGGGGCGATCAA
upper sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 6
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
| | | || | | || | | | | | || | || || | | || ||| || | || | ||| |||| |||| || ||||| || |||||||| ||||| || || ||||| || |||||||||||||||||||||||||| || ||||| || |||||||| ||||| |
----------------------------------------------------------------------------------------agccataaacatatcaataatttaatttggcattattttt--------tcttgtgtaaagtgatattgatttgaataaaaaatacttacgct-attcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA
upper sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA14G33410.1 (Glycine max), 3'ss of exon 5
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctc--tcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctt-tgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
|| ||| || || | | | | | |||| ||| | | ||| | | | |||| || || | ||| | |||| ||| ||||| || |||||||||||||| || ||||||||||| ||||| | ||| |||||||||||||| || |||||||| || || || |||||||| || || |
--------------------------------------------------------------------------------------------tgaaaggcaatagaatttgaatttcaacaatggatatgattatgcctttagaatatgtctgtttccat----tttgaaattattatatttctgtttt----ctcacagGTCAGTCATCATCCAATGATAGTTGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGAGATAGCAACTTAAAGAGTAAATTTTGGGGTCGGTCAA
upper sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA18G01590.1 (Glycine max), 3'ss of exon 5
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattag-aaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttca-------tctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
|| | ||||||| ||| || | | || || || | | ||| | | || | | || | || | | || || || |||| | | | | | || || ||| | | | ||| | ||| | | | | |||| | | || | ||||| || ||||||||||||||||| || |||||||| ||||| || || ||||| ||||||| || || |||||| | || || ||||| |||||||
--gtaactgggtttttccttt-aacttttcaatcaaggttaatgg-----gaatgagtcaaaatttacaggcaaatgcagcaacaataaacta---aaatatttgt---tgcttcattattgtgttttgttgttgaatctgaaatagggcagtgatttgtgtgtcttatgctgctaattttcttctaacaagaagcttgctccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGATGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
upper sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA11G37650.1 (Glycine max), 3'ss of exon 5
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttca-------tctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
|| | ||||||| ||| || | | || || || | | ||| | | || | | || | | || || || | | | |||| || | | ||||| | | | ||| | || | | | | |||| || | || | | ||||| || ||||||||||||||||| || |||||||| ||||| || || ||||| ||||||| || || |||||| | || || ||||| |||||||
--gtaactgggtttttccttttaacttttcaatcaaggttaatgg-----gaatgagtcaaagtttacaggcaaatgcggcaaaaaatagactaataaat-ttgttgcttcattcttgccttt-tgttattgaatctgaaaaagggcagtgatttgtgtctattgtatgctgctaattttcatctaacaagaagcttgttccagGTTAGTCATCATCCAATGATTGTTGCTTGTCACTGTGAGGGAAGGGGTTGGAAGTTTTGGGCAGATTCTAATTTGAAAGGAAAATTCTGGGGGCGTTCTA
upper sequence: PP1S18_231V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv18s0001g03790.t01 (Vitis vinifera), 3'ss of exon 5
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
| | ||| | | | ||| || | || ||| | || | |||| || || | |||| | | | ||| | || || || || | |||||| || ||||| || |||||||| ||||||||||| ||||| | || ||||||||||||| || ||||| || || ||||| |||||||| || ||||
-------------------------------------------------------------------------------------ataacatcagca--ttttattaaat--tctttggcattc-cagattaacttcttcagtagtaatta---tcaaataacc-aaggttgtcaattgtttttgttgag---tcagGTTAGTCATCACCCTATGATTGTTGCATGTCACTGTGAGGGTACGGGATGGAAATTTTGGGCAGATAGCAATTTAAAGAGCAAATTTTGGGGTCGGTCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
ttctttgtttttattt CT-rich tract
aagttctttgttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgatatggtttttgttttcaattgtatgatgcttttttgtgtcttatggacctgtcgcatctattagccttgtagctgaattttgaaatctgtagatgttagtatgtgctccttgtctctctcttattagaaattttaggtccggctgaaccgaaatgatctgaagttctttgtttttatttttcatctctcagGTGAGCCATCATCCAATGATTGTGGCATGTCACTGCGAGGGCAGAGGCTGGAAATTTTGGGGTGACAGCAACTTGAAAAGCAAGTTTTGGGGCCGTTCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG