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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattattcctcattacgagttaccaccagtgattatgtgaattggctgtgtggaactggtatgtggggctgatctaatgtcattacaagtgagttgctaattattattgtcgggttctgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAG

Basic information

species Physcomitrella patens
transcript PP1S83_234V6.4
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S83_234V6.4 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
gtattattcctcattacgagttaccaccagtgattatgtgaattggctgtgtggaactggtatgtggggctga-tctaatgtcattacaagtgagttgctaattattattgtcgggttctgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAG
                 |  ||  ||    |  | | ||   |||   ||   | ||    ||       ||| |  || | ||| || |      || |||||||| |   |   ||||     | || || ||||| |||||||||||| ||||||| ||||||||||| || || ||||| |||||| | || ||  | |||||||| |||||  |||||
-----------------ggatt--cattccttgtcaagtatcttgttagtaaagcac-atcataaatttttgaatagaaaggcataacta------tgttaattattttctgcaacttctct---ccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG

upper sequence: PP1S83_234V6.4 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 11
gtattattcctcattacgagttaccaccagtgattatgtgaattggctgtgtggaactggtatgtggggctgatctaatgtcattacaagtgagttgctaattattattgtcgggttctgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAG
            ||| | | ||      |  |||| ||| |||           ||    |   |    |   |  | | | | ||||      |||  |||||||  |  |   | ||     | || || ||||| |||||||||||| ||||||| ||||| ||||| || || ||||| |||||| | || ||  | |||||||| |||||  |||||
------------att-caatttcttgttaaagattctgttaat----------aaagctcttcatacatcc--ttgagtataaatacataactattgtcaattatttcttacaattgcttt---ccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGTAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGAGAAGGAGACAATGGCAAACAG

upper sequence: PP1S83_234V6.4 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 10
gtattattcctcat-tacgagttaccaccagtgattatgtgaattggctgtgtggaactggtatgtggggctgatctaatgtcattacaagtgagttgctaattattattgtcgggttctgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAG
           |||  || | | ||| |   ||   |   |||||   |   |    | |  ||     |   |||||    |  ||||| ||| ||||||           | ||||       | || || || || |||||||||||||| || || ||||| ||||| || |||||||| |||||| | || ||||| ||||| || ||||| ||||||
---------aacatgcacaattgacccctcatg--cactagaattcaattcat----cagtcatcacaagaacatctatgtactctacaaatgatttgcta--------caactggttt------ccagTGGCGAAAGTATGGAGAATGCACTACGTGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGTGACAATGGACAACAG

upper sequence: PP1S83_234V6.4 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
gtattattcctcattacgagttaccaccagtgattatgtgaattggctgtgtggaactggtatgtggggctgatctaatgtcattacaagtgagttgctaattattattgtcgggttctgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAG
                           ||   | ||   |||||   |   |   |     ||||  |      |  ||      | ||        ||    || |||  |     ||||   | || || || ||||||||||||||  | || || ||||| ||||| || |||||||| |||||| | || ||||| |||||||| ||||| ||||||
-------------------------ttcatgcacta---gaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactctgcaaatgatttgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG

upper sequence: PP1S83_234V6.4 (Physcomitrella patens), 3'ss of exon 11
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 11
gtattattcctcattacgagttaccaccagtgattatgtgaattggctgtgtggaactggtatgtggggctgatctaatgtcattacaagtga-gttgctaat-tattattgtcgggttctgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAG
                                                              |   |   | | || |     | | |  | | ||   || | ||| ||  |   ||     ||  |||||| ||||| |||||||| || ||  | || ||||||||||||||||| ||||| |||||| |||| ||| | ||||| || ||||| ||||||
-------------------------------------------------------------gtaaagaaatcagcttaaacactaatagttaacgtcaatactatataatgattttgtctctgaacatagCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAAGATTCTGATTCATAGAGAAGGCGACAATGGTCAACAG

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|162247261|gb|FC423059.1|FC423059
EST:     GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAG                         CGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
genomic: GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAGgtattattcc ... tgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
EST: gi|162155634|gb|FC331559.1|FC331559
EST:     GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAG                         CGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAG
genomic: GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAGgtattattcc ... tgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAG
EST: gi|162250016|gb|FC427117.1|FC427117
EST:     GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAG                         CGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
genomic: GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAGgtattattcc ... tgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
EST: gi|37826149|gb|BJ584161.1|BJ584161
EST:     GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAG                         CGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
genomic: GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAGgtattattcc ... tgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
EST: gi|162154986|gb|FC331404.1|FC331404
EST:     GCAAACAACTTTGTGGTGTCTCCATAATAAGGAG                         CGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
genomic: GCAAACAACTTTGTGGTGTCTCCATAATAAGGAGgtattattcc ... tgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
EST: gi|162159567|gb|FC335745.1|FC335745
EST:     GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAG                         CGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
genomic: GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAGgtattattcc ... tgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
EST: gi|162250017|gb|FC427118.1|FC427118
EST:     GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAG                         CGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
genomic: GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAGgtattattcc ... tgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
EST: gi|162247262|gb|FC423060.1|FC423060
EST:     GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAG                         CGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
genomic: GTTGGAGTAGACTTCTGCAAACAACTTTGTGGTGTCTCCATAATAAGGAGgtattattcc ... tgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
EST: gi|37837126|gb|BJ595134.1|BJ595134
EST:     CCATAATAAGGAG                         CGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT
genomic: CCATAATAAGGAGgtattattcc ... tgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaatgtcattacaagtgagttgctaattattattgtcgggttctgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAG
                      tgctaat  putative branch site (score: 2)
                     ttgctaattattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattattcctcattacgagttaccaccagtgattatgtgaattggctgtgtggaactggtatgtggggctgatctaatgtcattacaagtgagttgctaattattattgtcgggttctgcaaactagCGGGGAGAGCATGGAGAATGCACTGCGGGCGTGCTGCAAAGGCATCAAGATTGGAAAGATTTTGATACATCGCGAAGGAGATAATGGGCAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT