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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgctcggttgttatggcccaccataaaccctaagctcgtcatcactgctggtaatcaatgactactacaactttgacgattttagtcttggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG

Basic information

species Physcomitrella patens
transcript PP1S154_6V6.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S154_6V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 10
ttgctcggttgttatggcccaccataaaccctaagctcgtcatcactgctggtaatcaatgactactacaactttgacgattttagtcttggattta-cagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG
 | || |     | | |   ||     |  || | ||    ||  ||  |||||||   | |||| || |        | |  |    || | |||  ||||| || || |  |||||  |  |    ||   |||||||||||| |||||||| ||||||||||| ||| |||| || |||||||||||  |||||||||
gtact-gaccaatcttgtgtactgctgaagctgaact----attgct--tggtaatt--ttactaatatattcaatgtgctcgttccatttgctttgtcagGCTGCTGTTACAGCACTTCAAAACCAACCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTATGTTGACATCAGTGTTGCTGTTG

upper sequence: PP1S154_6V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os02g31040.1 (Oryza sativa), 3'ss of exon 9
----------------------------------------------ttgctcggttgttatggcccaccataaaccctaagctcgtcatcactgctggtaatcaatgactactacaactttgacgattttagt---------cttggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG
                                              |  |||    ||  | |   |  | ||| |  || ||  | |    | ||  ||| | || | |    ||| | ||  | || || |         ||||  ||| ||||| || ||   ||| ||  |  |    ||   ||| |||||||| |||||||| ||||||||||||||| | || ||| ||||||||||  |||||||||
gtaatgtttacccctttttttcttcttcttaatataatgatacacatctctctcgcgtgttcgagaaaaaaaaaacgcaatcttatga--gatact--taaaccataattgtggcaattgtgtgggttgtactaaaaacccacttgcttttgcagGCTGCTGTTTCTGCGCTTCAAAACCAACCAATTGTTAATGCTGTCATTGATGGTGATGACATCATCTACAGGGAGTACATTGACATCAGTGTTGCTGTTG

upper sequence: PP1S154_6V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM2G079538_T02 (Zea mays), 3'ss of exon 11
ttgctcggttgttatggcccaccataaaccctaagctcgtcatcactgctggtaatcaatgactactacaactttgacgattttagtcttggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG
                          |  | || ||    ||   ||  ||   | ||   |||  ||      || | | ||   | |||  ||   |||| || ||   ||||||  |  |    ||   |||||||||||| |||||||| ||||||||||| ||| |||| ||||| ||||||||  |||||||||
-----------------gtatttgccagtcttaggcgttgcaaagcttttgc--accat--acttttatgtggctggctaattatat-ttgttttggtagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTCAATGCTGTCATTGATGGTGATGACATCATATACAGAGACTACGTAGACATCAGTGTTGCTGTTG

upper sequence: PP1S154_6V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM5G807639_T03 (Zea mays), 3'ss of exon 10
ttgctcggttgttatggcccaccataaaccctaagctcgtcatcactgctggtaatcaatgactactacaactttgacgattttagtcttggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG
                        | |  | || |     ||   ||  ||  || ||   | |  ||   ||  |   ||||||   ||   ||  ||||| || ||   ||||||  |  |    ||   ||| |||||||| |||||||| ||||||||||| ||| |||| ||||| ||| ||||  |||||||||
--------------------gtacttagtcttatgtgttgcaaagcttttg--aaccatacatttatatggctg-gctaatttta--tttattttgtcagGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTTAATGCTGTCATTGATGGCGATGACATCATATACAGAGACTACGTAGACGTCAGTGTTGCTGTTG

upper sequence: PP1S154_6V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GRMZM5G807639_T02 (Zea mays), 3'ss of exon 10
ttgctcggttgttatggcccaccataaaccctaagctcgtcatcactgctggtaatcaatgactactacaactttgacgattttagtcttggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG
           | | ||  |    | |  | || |     ||   ||  ||  || ||   | |  ||   ||  |   ||||||   ||   ||  ||||| || ||   ||||||  |  |    ||   ||| |||||||| |||||||| ||||||||||| ||| |||| ||||| ||| ||||  |||||    
-----------tcaaggtac----ttagtcttatgtgttgcaaagcttttg--aaccatacatttatatggctg-gctaatttta--tttattttgTCAGGCTGCTGTTTCTGCACTTCAAAACCAGCCAATTGTTAATGCTGTCATTGATGGCGATGACATCATATACAGAGACTACGTAGACGTCAGTGTTGCT----

upper sequence: PP1S154_6V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ31629 (Selaginella moellendorffii), 3'ss of exon 6
ttgctcggttgttatggcccaccataaaccctaagctcgtcatcactgctggtaatcaatgactactacaactttgacgattttagtcttggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG
                                    ||| | |   |   |  | ||||    | ||     ||||  ||    || | |   |||  |||| || || || ||  |  ||      || | ||| || ||||| || || |||||||||||||| ||| |||| ||||| |||||||||||||||||||
--------------------------------gtattcggcgtggattgcgtaattcaagagtttct----ttttgctgac---agacgtcatttt--agGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG

upper sequence: PP1S154_6V6.2 (Physcomitrella patens), 3'ss of exon 10
lower sequence: EFJ38519 (Selaginella moellendorffii), 3'ss of exon 6
ttgctcggttgttatggcccaccataaaccctaagctcgtcatc-actgctggtaatcaatgactactacaactttgacgattttagtcttggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG
                                    ||| | |  | ||||   | ||||    | ||     ||||  ||    || | |   |||  |||| || || || ||  |  ||      || | ||| || ||||| || || |||||||||||||| ||| |||| ||||| |||||||||||||||||||
--------------------------------gtattcggcgtggattgctta-attcaagagtttct----ttttgctgac---agacgtcatttt--agGCTGCTGTTAGCGCTTTGCAGGCGCAGCCCGTTGTAAACGCTGTGATCGACGGAGATGACATCATTTACAGAGACTACGTCGACATCAGCATTGCTGTTG

Mapped 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|208368131|gb|DC947691.1|DC947691
EST:     TGGGANTTATGTC-NGA-TTGTT-AG                         GCAGCCGTGAGTGCACTCAAGCAA-TTCCTGCTGTCAATGCTGTAATTGAT
genomic: TGGGATTTATGTCTGGATTTGTTAAGgtacccgagt ... ggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGAT
EST: gi|162156510|gb|FC332118.1|FC332118
EST:     TTCAAGAGAAGCACGGTGTGAAATTGGGATTTATGTCTGGATTTGTTAAG                         GCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGAT
genomic: TTCAAGAGAAGCACGGTGTGAAATTGGGATTTATGTCTGGATTTGTTAAGgtacccgagt ... ggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGAT
EST: gi|162163854|gb|FC340076.1|FC340076
EST:     TTCAAGAGAAGCACGGTGTGAAATTGGGATTTATGTCTGGATTTGTTAAG                         GCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGAT
genomic: TTCAAGAGAAGCACGGTGTGAAATTGGGATTTATGTCTGGATTTGTTAAGgtacccgagt ... ggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgctggtaatcaatgactactacaactttgacgattttagtcttggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG
                          ctttgac  putative branch site (score: 4)
       taatcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgctcggttgttatggcccaccataaaccctaagctcgtcatcactgctggtaatcaatgactactacaactttgacgattttagtcttggatttacagGCAGCCGTGAGTGCACTCAAGCAATTTCCTGCTGTCAATGCTGTAATTGATGGAGATGACATCATCTACCGAGATTACGTTGACATCAGCATTGCTGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT