Sequence
atgc intronic sequence ATGC exonic sequence...agacgtaaggtgctccgaagtttctctgtgttagtgatctgacactaacagtgtattttgtactgcgatctactgagactcggtgttgaaatttgcacagTATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCTGTTCACATTCCAAACCACAAGTTCAGTGTAAGTGTAGTCCGTAATTTGA
Basic information
species | Physcomitrella patens |
transcript | PP1S79_156V6.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: PP1S79_156V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA09G33170.1 (Glycine max), 3'ss of exon 10
---------------------------------------------agacgtaaggtgctccg-aagtttctctgtg-----ttagtgatctgacacta------acagtgta---ttttgtactg------cgatctactgagactcggtgttgaaat-ttgcacagTATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCTGTTCACATTCCAAACCACAAGTTCAGTGTAAGTGTAGTCCGTAATTTGA
| | || || || | |||| | ||| ||| || | || | ||||| || ||| | ||| |||| | | |||| || | ||| ||||||| |||||||| || || | |||||||| || |||||||||||||||||||||||||||||||| || | || | ||| || || || | |
gtgtgttatactgcaccttttaacctttgaatgtgggaattacttacattaaatatgtaccatatgtttttgtgtaataacttaacagatggaaattatgaaatatggtgtagtgcttgatacccttgagtcattcttttgagcattgatgttttcatgctatgcagCATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCTGTTCACATTCCAAACCACAAATTTACAGTGAATGTTGTGCGGAACCTTA
upper sequence: PP1S79_156V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 10
----------------------------agacgtaaggtgctccgaagtt---tctctgtgttagtgatctgacactaacagtgtattttgtactgcgatctactgagactcggtgttgaaat-ttgcacagTATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCTGTTCACATTCCAAACCACAAGTTCAGTGTAAGTGTAGTCCGTAATTTGA
| || | || | || | | | || | | | ||| | || | | | | ||| |||| | | |||| || || ||| ||||||| |||||||| || || | |||||||| || |||||||||||||||||||||||||||||||| || | || | ||| || || || | |
gtgtgttgtactgtaccttttaacttttgaatgtgggaatttcttacattaaatatgtacaatattttttgtgtaataatcg-atacccttgagt-cattcttttgagcattgatgttttcatgctgtgcagCATGTTGGCTGGTGGTCACCAACAATTATTAGAGGTGAAGATCGTGAAGCTGTTCACATTCCAAACCACAAATTTACAGTGAATGTTGTGCGGAACCTTA
upper sequence: PP1S79_156V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv18s0001g07500.t01 (Vitis vinifera), 3'ss of exon 10
agacgtaaggtgctccgaagtttctctgtgttagtgatctgacactaacagtgt-----attttgtactgcgatctactgagactcggtgttgaaatttgcacagTATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCTGTTCACATTCCAAACCACAAGTTCAGTGTAAGTGTAGTCCGTAATTTGA
|| | | | || |||| | | | || | | | | |||| | | | | | | || | ||| ||| |||| ||||||||||| ||||| | || ||||| |||||||| ||||| |||||||||||||||||||| |||| || | ||| || | ||| | |
-----tataatatgggagattaacttcgtgtgatcatgaaggccacaataatttcaacaaccttgtctctctgttttttaatgataataattcatattacttcagCATGTGGGTTGGTGGTCACCGACAATCATAAGAGGTGATGATCGGGAAGCAGTTCACATTCCAAACCACAAATTCACAGTGAATGTTGTGAGGAATCTTA
upper sequence: PP1S79_156V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv00s0313g00020.t01 (Vitis vinifera), 3'ss of exon 10
agacgtaaggtgctccgaagtttctctgtgttagtgatctgacactaacagtgtattttgtactgcgatctactgagactcggtg---ttgaaatttgcacagTATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCTGTTCACATTCCAAACCACAAGTTCAGTGTAAGTGTAGTCCGTAATTTGA
|| | | || | | ||| || || | | | | || || | | || |||| | | | || | |||| |||| || |||||||| || || | | ||||| || ||||||||||| || |||||||||||||||||||||| ||| | ||| || | ||| | |
---agttaagaaatcggttgcctctttgaattggaaaatgatgagatgccaagtcagatgcatttttattgtctgaattttgataatcttttgttgcctacagCATGTGGGATGGTGGTCACCAACAATAGTAAGAGGTGAAGATCGTGAAGCAGTCCACATTCCAAACCACAAGTTCACTGTGAATGTTGTGAGAAATCTCA
upper sequence: PP1S79_156V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv18s0001g07520.t01 (Vitis vinifera), 3'ss of exon 7
agacgtaaggtgctccgaagtttctctgtgttagtgatctgacactaacagt-gtattttgtactgcgatctactgagactcggtgttgaaatttgcacagTATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCTGTTCACATTCCAAACCACAAGTTCAGTGTAAGTGTAGTCCGTAATTTGA
| || || | ||| | || || || | | || || | |||| | | | | | | | | ||| ||| ||| ||||||||||| ||||| | || ||||| |||||||||||||| ||||| |||||||| |||| |||| || | ||| || | ||| | |
-aaaaaaaaaagcaacttggttgttttgcaatatgaataaggtaggaattgtcagaccttgtctttctgcttttttgtaattataatacatattacttcagCGTGTGGGTTGGTGGTCACCGACAATCATAAGAGGTGATGATCGTGAAGCAGTTCATGTTCCAAACAACAAATTCACAGTGAATGTTGTGAGGAATCTCA
upper sequence: PP1S79_156V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ29482 (Selaginella moellendorffii), 3'ss of exon 6
agacgtaaggtgctccgaagtttctctgtgttagtgatctgacactaacagtgtattttgtactgcgat-ctactgagactcggtgttgaaatttgcacagTATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCTGTTCACATTCCAAACCACAAGTTCAGTGTAAGTGTAGTCCGTAATTTGA
| | || | | ||| | || |||| | | |||| |||| || | || |||||||||||||| ||||| ||| |||| ||||| || ||||| || || ||||| || |||||||||| || || || || | || | |
---------------------------------------gtatgttgtcaaaggaccttgaaggaaaatgttactaaaattcggc--------ttgc-tagCACGTCGGTTGGTGGTCTCCAACTGTCATTCGAGGTGATGACCGCGAAGCCGTCCATATTCCTAATCACAAGTTCACCGTGAGCGTCGTTAGGAACCTTA
upper sequence: PP1S79_156V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EFJ28057 (Selaginella moellendorffii), 3'ss of exon 5
agacgtaaggtgctccgaagtttctctgtgttagtgatctgacactaacagtgtattttgtactgcgat-ctactgagactcggtgttgaaatttgcacagTATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCTGTTCACATTCCAAACCACAAGTTCAGTGTAAGTGTAGTCCGTAATTTGA
| | || | | ||| | || |||| | | |||| |||| || | || |||||||||||||| ||||| ||| |||| ||||| |||||||| || || ||||| || |||||||||| || || || || | || | |
---------------------------------------gtatgttgtcaaaggaccttgaaggaaaatgttactaaaattcggc--------ttgc-tagCACGTCGGTTGGTGGTCTCCAACTGTCATTCGAGGTGATGACCGTGAAGCCGTCCATATTCCTAATCACAAGTTCACCGTGAGCGTCGTTAGGAACCTTAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|162190538|gb|FC366176.1|FC366176EST: GGTGTCTGGTACTGTTGAG TATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCT
genomic: GGTGTCTGGTACTGTTGAGgttaggcttt ... atttgcacagTATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taacagtgtattttgtactgcgatctactgagactcggtgttgaaatttgcacagTATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCTGTTCACATTCCAAACCACAAGTTCAGTGTAAGTGTAGTCCGTAATTTGA
cactaac putative branch site (score: 1)
tattttgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agacgtaaggtgctccgaagtttctctgtgttagtgatctgacactaacagtgtattttgtactgcgatctactgagactcggtgttgaaatttgcacagTATGTTGGTTGGTGGTCTCCGACTGTGATTAGAGGAGATGATCGTGAAGCTGTTCACATTCCAAACCACAAGTTCAGTGTAAGTGTAGTCCGTAATTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgaa