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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattgttaggattaagctctgttcaatttggcgctgtaacgaattctcctttccgctcagacagacctcgtatggaatctggtgtgtggtccgcgatggaggtttcgcacatgtttgttcgcctctcggaatagctcatacggaaagataactgaatgatttttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC

Basic information

species Physcomitrella patens
transcript PP1S306_43V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G109624_T01 (Zea mays), 3'ss of exon 4
gtgattgttaggattaagctctgttcaatttggcgctgtaacgaattctcctttccgctcagacagacctcgtatggaatctggtgtgtggtccgcgatggaggtttcgcacatgtttgttcgcctctcggaatagctcatacggaaagataactgaatgatttttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC
                                                                       ||| |  || ||   | |    |   ||  |       ||| |  |   |    ||| | ||| |   |||   || | |    |  |||  | |     |||   ||| |  | ||||||||||| | |||||||| ||||||||||| ||||| || ||||| || || ||  | ||||||||| ||||||| ||||  ||||   || | ||||
-----------------------------------------------------------------------gtacgccatttgccatctttggcctcatataa------cacttagtcacttatttctagaaatggaagata-acaatgctgg--ggctgaagtcttgaacttatcttgtataac-agGCAAAATGCTTGGAAACTGGTGAGACGGTGGCGATAAAAAAGGTGTTACAAGATAAGCGCTACAAGAATAGAGAGCTCCAGACTATGCAGTTGCTTGACC

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G155836_T01 (Zea mays), 3'ss of exon 4
gtgattgttaggattaagctctgttcaatttggcgctgtaacgaattctcctttccgctcagacagacctcgtatggaatctggt-gtgtggtccgcgatggaggtttcgcacatgtttgttcgcctctcggaatagctcatacggaaagataactgaatgatttttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC
                                                   |||      | ||| | |  ||||| ||     |  | ||||      || ||  ||  ||| |   |  |  |       |||||||| | |          |    |  ||| |     | ||||    |   ||||| || ||  | |||||||| ||||| || |||||||| || ||  | || ||||| |||||||||||||| |||||||| | ||||||| || | ||||
--------------------------------------------------gtttgttactatacaaatca-gtatgaaactgaattatctggtttttattgtagtattt-cacttaggtagtaact------aatagctccttcc---------cctctttttttataaaaataaatgatcttgtacagGCCAAGTGTCTTGAAACTGGTGAGACCGTAGCTATAAAAAAGGTTCTTCAAGACAAGAGATACAAGAATCGTGAGCTGCAAACCATGCGAGTGCTTGACC

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA04G06760.1 (Glycine max), 3'ss of exon 3
gtgattgttaggattaagctctgttcaatttggcgctgtaacgaattctcctttccgctcagacagacctcgtatggaatctggtgtgtggtccgcgatggaggtttcgcacatgtttgttcgcctctcggaat---agctcatacggaaagataactgaatgatttttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC
                                                                                                | |   || ||   ||  | ||  |   |||| |   |     |  || | |  | |   |||| | | |||| | |                ||||||||||| | |||||||||||| | ||||| || || || || ||||| |||| ||||||||||||||| || || ||| | |||||  || |||| |
--------------------------------------------------------------------------------------------gtatgttaatggcttaatactagattcatttactcttgctgtctccacctattctgccaaaatgctga-taactttttctt----------------agGCAAAATGCTTGGAAACTGGGGAGGCAGTGGCAATTAAAAAGGTTTTGCAAGACAGAAGATACAAGAATCGTGAACTACAGTTAATGCGTGTGATGGATC

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA15G09090.1 (Glycine max), 3'ss of exon 3
gtgattgttaggattaagctctgttcaatttggcgctgtaacgaattctcctttccgctcagacagacctcgtatggaatctggtgtgtggtccgcgatggaggtttcgcacatgtttgttcgcctctcggaatagctcatacggaaagataactgaatgatttttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC
                                                                                                | ||          ||  | || ||  | ||| |   |  ||   ||     ||||| |   || ||| |                |   ||||||||||| | |||||||||||  | |||||||| || || || || ||||||| ||||||||||||||| || || ||| | |||||  | ||||| |
--------------------------------------------------------------------------------------------gtatggtgataaccaactactagattctttac-tcttgctgtcactaccacatgctgataatt---tgttttct---------------ctcttagGCAAAATGCTTGGAAACTGGGGAAGCAGTGGCTATTAAAAAGGTTTTACAGGACAGAAGATACAAGAATCGCGAACTACAGTTAATGCGTGTTTTGGATC

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA06G06850.1 (Glycine max), 3'ss of exon 3
gtgattgttaggattaagctctgttcaatttggcgctgtaacgaattctcctttccgctcagacagacctcgtatggaatctggtgtgtggtccgcgatggaggtttcgcacatgtttgttcgcctctcggaatagctcatacggaaagataactgaatgattt-ttgcgtgttaatg-tgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC
                                                                                                            | |      ||  |   |    || |   | |  |     | |  |    |  |||      || | ||  | | ||  |||||||||||| | |||||||||||| | ||||| || || || || || || |||| ||||||||||||||| || |||||| | |||||  || |||| |
------------------------------------------------------------------------------------------------------------gtatgctaatggcctaatactagattcatttactcttgctg-tcgccacctattttgccaaatgctgataattttttctcagGCAAAATGCTTGGAAACTGGGGAGGCAGTGGCAATTAAAAAGGTTTTACAAGACAGAAGATACAAGAATCGTGAACTGCAGTTAATGCGTGTGATGGATC

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G61160.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgattgttaggattaagctctgttcaatttggcgctgtaacgaattctcctttccgctcagacagacctcgtatggaatctggtgtgtggtccgcgatggaggtttcgcacatgtttgttcgcctctcggaatagctcatacggaaagataactgaatgatttttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC
                                                                                       ||        ||  ||  |    | || ||  || |    |   || |  | ||   |||           |||||  || || || ||||        |||| || ||| | || || |  || |  || || |||||||||||||| |||||||| |||||||| ||  |||| || |||||||||||| || | || |
---------------------------------------------------------------------------------------gtaaataa-aatttagactcgagatattttatttagttgttttaaaaatttgattttgaagt---------tgattcctg-gttttgatgt--------agGCTAAGTGCTTAGAGACGGAAGAAAAAGTAGCAATAAAGAAAGTGTTACAGGACAAGAGATACAAAAACAGAGAACTTCAGATCATGCGAATGCTTGATC

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 3
gtgattgttaggattaagctctgttcaatttggcgctgtaacgaattctcctttccgctcagacagacctcgtatggaatctggtgtgtggtccgcgatggaggtttcgcacatgtttgttcgcctctcggaatagctcatacggaaagataa-ctgaatgatttttgcgt--gttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC
                                                                                                            | |||||  | ||       |  | ||  |    |   |  ||   ||  ||  ||  ||  |  |||  |   |  ||  ||||||||||| | |||||||| ||||| ||||| |||||||| || |||||||||| |||||| |||||||| ||||||||| | |||||   | |||| |
------------------------------------------------------------------------------------------------------------gtacatggatattaattatgcaaactatttgtgtcaatatcattttctttatatttcatgtcttggttcctcgcttctgttagGCAAAATGCTTGGAAACTGGAGAGACTGTGGCCATAAAGAAGGTTTTGCAGGACAGAAGATATAAGAATCGTGAGCTGCAGTTAATGCGCACGATGGATC

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 3
gtgattgttaggattaagctctgttcaatttggcgctgtaacgaattctcctttccgctcagacagacctcgtatggaatctggtgtgtggtccgcgatggaggtttcgcacatgtttgttcgcctctcggaatagctcatacggaaagataactgaatgatttttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC
                                                                                                                      ||  ||      |  |   |||| |   | | ||||       ||| | | ||||    |    |  ||||| || ||| ||||||| || ||||||||||| || ||||| ||||| |||||||| |||||||| || || |||||||| || ||||| ||  | ||||
----------------------------------------------------------------------------------------------------------------------gtgtgcaaactcgctttaatcattct--aggctaac------gtttcttcctgttgggcttcact-tcagGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCCATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC

upper sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 3
gtgattgttaggattaagctctgttcaatttggcgctgtaacgaattctcctttccgctcagacagacctcgtatggaatctggtgtgtggtccgcgatggaggtttcgcacatgtttgttcgcctctcggaatagctcatacggaaagataactgaatgatttttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC
                                                                                                                      ||  ||      |  |   |||| |   | | ||||       ||| | | ||||    |    |   |||| || ||| ||||||| || |||||||||||||| ||||| ||||| |||||||| |||||||| || || |||||||| || ||||| ||  | ||||
----------------------------------------------------------------------------------------------------------------------gtgtgcaaactcgctttaatcattct--aggctaac------gtttcttcctgttgggcttcact-ttagGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCTATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC

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|162196892|gb|FC373297.1|FC373297
EST:     ATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAG                         GCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAG
genomic: ATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAGgtgattgtta ... gtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAG
EST: gi|100387363|gb|BY970507.1|BY970507
EST:     ATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAG                         GCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAG
genomic: ATTCGGCAGAACGTGTTGTTGGCACTGGATCATTCGGGATTGTCTTCCAGgtgattgtta ... gtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctcatacggaaagataactgaatgatttttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC
                                    tgttaat  putative branch site (score: 3)
                       aatgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattgttaggattaagctctgttcaatttggcgctgtaacgaattctcctttccgctcagacagacctcgtatggaatctggtgtgtggtccgcgatggaggtttcgcacatgtttgttcgcctctcggaatagctcatacggaaagataactgaatgatttttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA