Sequence
atgc intronic sequence ATGC exonic sequence...gcgagggatgagagcttggatctttttgtcatattccagtttagtatgctaacaaagactataataattgacctttggatacatgtggtgtgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
Basic information
species | Physcomitrella patens |
transcript | PP1S68_31V6.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G080083_T02 (Zea mays), 3'ss of exon 6
--------------gcgagggatgagagcttggatctttttgtcatattccagtttagtatgctaacaaag--actataataattgacctttggataca-------tgtggtgtgcgac-----gcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
| | | | || | | || ||| | || ||| ||| | ||| | || ||| | | | | ||| | | || || | | || ||||| |||||||| ||||||||||| || || |||||||| |||||| ||||| | ||||| ||||| | |||||||| || | || | ||
gtgacaccttcaaatcatgttctaacagttctgctcctttgtattttctcaagtgcagtttttcttcaatggaaccctaagcttccattatgcaacacactgaacttcttgtttgtgtttccctgtagGTATTTCTCATATGAGCATTTCTATGTGATATATTGCAAGTTCTGGGAGCTGGACACCGATCATGACTTCTTTATTGACAAAGAAAATCTTATTAAGTAT
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA19G43790.1 (Glycine max), 3'ss of exon 7
------------------------gcgaggga--tgagagcttggatctttttgtcat-attccagtttagtatgctaacaaagactataataattgacctttggatacatg----tggtgtgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
| | | | ||| || | ||| |||||| |||| | | | || | | ||| || | | || ||| | | ||| |||| || || || ||||| ||||| |||||||| |||||||||||||||||| |||| | ||||| || || |||| ||||| || | || | ||||
gtagatataattgaaaatgtcatttcaattaacttcagaaaatg-accttggtgtcattattcaaatgaactaaatatatttgtattatgatgccttaatcttttttacctttccttaatgttatctgcagGTACTTCTCTTATGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA20G35090.1 (Glycine max), 3'ss of exon 7
gcgagggatgagagcttggatctttttgtcatattccagtttagtatgct-aacaaagactataataattgacctttggatacatgtggtgtgcgacg------cagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
|| | ||| | | || ||| || |||| | || || | | | | | | || | | ||| | | ||| ||| || || |||||||| ||||| ||||| ||||||||||| ||||||||| | ||| | ||||| |||||| | ||||| | || |||| | |||
-----aaattcatgattgactttcattttcaattt--agttctctctgtagaattgaaattttcttgtctttttatttgcttcattaattatcttacggaatttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA10G32500.1 (Glycine max), 3'ss of exon 7
gcgagggatgagagcttggatctttttgtcatattccagtttagtatgct-aacaaagactataataattgacctttggatacatgtggtgtgcgacg------cagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
|| | ||| | | || ||| || |||| | || || | | | | | | || | | ||| | | ||| ||| || || |||||||| ||||| ||||| ||||||||||| ||||||||| | ||| | ||||| |||||| | ||||| | || |||| | |||
-----aaatccatgattgactttcattttcaattt--agttctctctgtagaattgaaattttcttgtctttgtatttgcttcattaattatcttacgaaatttcagGTACTTCTCATATGAGCATTTTTATGTCATTTACTGCAAATTTTGGGAGCTCGACACAGATCATGACTTTTTCATTGATAGAGAGAACCTTATTAAATAT
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA03G41180.1 (Glycine max), 3'ss of exon 7
------------------------gcgaggga--tgagagcttggatctttttgtcatattccagtttagtatgctaacaaagactataataattgacctttggatacatgt----ggtgtgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
| | | | ||| || | || ||||| | | || | | ||| || | | || ||| | | | | |||| || || || || || ||||| |||||||| |||||||||||||||||| |||| | ||||| || || |||| ||||| || | || | ||||
gtagatataattgaaaatttcatttcaattaacttcagaaaatgaccttggtttcattattcaaacgaactaaatatatttgtattatgatgccttaatcttttttacctttcctaaatattatctgcagGTACTTCTCTTACGAGCATTTTTATGTTATATACTGCAAGTTTTGGGAGCTGGATACAGATCATGATTTCTTGATAGACAAAGAGAATCTCATCAGATAT
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 3'ss of exon 6
gcgagggatgagagcttggatctttttgtcatattccagtttagtatgctaacaaagactataataattgacctttggatacatgtggtgtgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
| || | | | | ||| || || | | || | | | || | |||| ||| | | | || | || || || |||||||| ||||||||||| || ||||||||||| |||||| |||| |||||||||| || |||||||||| || | || || ||||
-gtactgacaaaaac----aaatttgtgctattgttgtatatatggtattgtttctgctcatttaacatgacttttctacttactt----tggcaaatagATACTTCTCATATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGAGATAT
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT1G54450.1 (Arabidopsis thaliana), 3'ss of exon 7
gcgagggatgagagcttggatctttttgtcatattccagtttagtatgctaacaaagactataataattgacctttggatacatgtggtg-tgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
|| |||| || |||||| | | | | | || | | | ||| | | | || || || || || ||||||||||||||||| || ||||||||||| ||||||||||| | ||||| || || | || ||||| || | || | |||||
---------------------gttggtgtcttaagattaattagtaatatgaaattggtgcttattaacggcttttattaagactctctactgtttattagGTACTTCTCGTATGAACATTTCTATGTCATATACTGCAAGTTCTGGGAGTTGGATACAGATCATGATTTCTTAATCGACAAAGAGAATCTCATCCGATAT
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 3'ss of exon 7
gcga-gggatgagagcttggatctttttgtcatattccagtttagtatgctaacaaagactataataattgacctttggatacatgtggtgtgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
| | | | ||| | | |||| |||| | |||||| | | ||| | | || ||| || || | | || | || || || || ||||| ||||||||||| || ||||||||||| |||||| |||| |||||||||| || |||||||||| || | || |||||||
gtactgacaaaaatatttgcgtgctattgttgtatt----tatagtattgtttttgctcatttaaca--tcacttttctattcactttg---gcaat-tagATACTTCTCGTATGAGCATTTCTATGTCATATACTGCAAGTTCTGGGAGCTGGATACGGATCACGATTTCCTGATTGACAAAGAAAATCTTATGCGATAT
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv07s0005g03730.t01 (Vitis vinifera), 3'ss of exon 8
-gcgagggatgagagcttggatctttttgtcatatt-ccagtttagtatgctaacaaagactataataattgacctttggatacatgtggtg--tgcgac-gcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
| | || | || || | ||||| |||| || ||| | || | || || | |||| | || ||||| | | | || |||| || ||||| |||||||| ||||||||||| ||||||||||| |||||| ||||| | ||||| || || |||||||||| || | || | ||||
aacaacagagagacacatgcatatatttgttttattattagattaactagttatttatgatgatga--attg---ctaggccccatgtcttcacttcaactgcagGTACTTTTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGACACAGATCATGATTTCTTGATTGACAAAGAGAATCTCATCAGATAT
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: Vv14s0036g00750.t01 (Vitis vinifera), 3'ss of exon 4
---gcgagggatgagagcttggatctttttgtcatattccagtttagtatgctaaca--aagactataataattgacctttggatacatgtggtgtgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
| |||| | | ||||| ||| | | || | |||| || || || || || ||| ||| ||| | | || || || || |||||||| ||||||||||| ||||||||||| |||||| |||| | || || || ||| ||||||| || || ||||| | ||||
tatttgtgggaatactctcataacatttttagcatgtact-gtgtggtattaaaattttaacaccattgcttttttttttttgat-tatgccct---taccatagGTACTTCTCTTATGAACACTTCTATGTTATATACTGCAAGTTCTGGGAGCTGGATACCGACCATGATTTTTTGATTGATAAAGAGAACCTAATCAGATAT
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ20642 (Selaginella moellendorffii), 3'ss of exon 7
gcgagggatgagagcttggatctttttgtcatattccagtttagtatgctaacaaagactataataattgacctttggatacatgtggtgtgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
|| | ||| ||| ||| ||| |||| ||| |||| | | || |||||||| || ||||| || || ||||| |||||||||||||||||| | ||| |||| |||||||| | || |||||| |||||| ||| |||||
----------------------------------------gtaa-gtcctattcgaga-tatc-caatatgtttttgctgaca-gtgggatac----tagATATTTTTCCTACGAACACTTTTACGTTATCTACTGCAAGTTTTGGGAGCTTGACACGGACCACGACTTCTTAATCGACAAGACTGACCTTTTGAGATAC
upper sequence: PP1S68_31V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ32791 (Selaginella moellendorffii), 3'ss of exon 7
gcgagggatgagagcttggatctttttgtcatattccagtttagtatgctaacaaagactataataattgacctttggatacatgtggtgtgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
|| | ||| ||| | ||| |||| ||| |||| ||| || |||||||| || ||||| || || ||||| |||||||||||||||||| | ||| |||| |||||||| | || |||||| |||||| ||| |||||
----------------------------------------gtaa-gtcctattcgagat----acaatatgtttttgctgaca-gtgggatgc----tagATATTTTTCCTACGAACACTTTTACGTTATCTACTGCAAGTTTTGGGAGCTTGACACGGACCACGACTTCTTAATCGACAAGACTGACCTTTTGAGATAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgctaacaaagactataataattgacctttggatacatgtggtgtgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
aaagactataataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcgagggatgagagcttggatctttttgtcatattccagtttagtatgctaacaaagactataataattgacctttggatacatgtggtgtgcgacgcagCTATTTTTCATATGAACATTTCTATGTTATTTACTGCAAGTTTTGGGAGTTGGACTCGGATCACGACTTTGTGATTGACAAGGATGACCTATTGCGATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG