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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggtttttttatgtctgtccaccacaataggcctagatattcaatttgaatttaacttgggagtaaaaagcacccagctactcggaataatggttgtagtcacttcatgcaagattgtaacgctcgtgactagtcttccagtgcataattttttgacagGTAAAAAACCCATGGCCGAATGTAGATGCTCATAGTGGAGTATTGCTTCAACACTATGGTCTGAAAGAACAGAA

Basic information

species Physcomitrella patens
transcript PP1S163_94V6.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S163_94V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
gtacggtttttttatgtctgtccaccacaataggcctagatattcaatttgaatttaacttgggagtaaaaagcacccagctactcgg--aataatggttgtagtcacttcatgcaagattgtaacgctcgtgactagtcttccagtgcataattttttgacagGTAAAAAACCCATGGCCGAATGTAGATGCTCATAGTGGAGTATTGCTTCAACACTATGGTCTGAAAGAACAGAA
                                                                               || ||| |    || ||| |||    |  || |||      |     |||    | |         || |||| ||      ||||| |||||||||||||| ||||| |||||||| ||||||||  ||||  | |||| |||  |    |||     
--------------------------------------------------------------------------gtaatgccactagattgatcatgattgctaccgttttatgtccatcttattggctaaaaagtgacaacattgtccatatttc-----cagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: PP1S163_94V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
gtacggtttttttatgtctgtccaccacaataggcctagatattcaatttgaatttaacttgggagtaa-aaagcacccagctactcggaataatggttgtagtcacttcatgcaagattgtaacgctcgtgactagtcttccagtgcataattttttgacagGTAAAAAACCCATGGCCGAATGTAGATGCTCATAGTGGAGTATTGCTTCAACACTATGGTCTGAAAGAACAGAA
                                                                 ||||    | |||    |  ||  |||     ||  | ||  ||  |   ||  |     | |  |||  |    ||   |||  | | ||||  ||||| || ||||| ||||||||||| |||||||| |||||||| |||||  | |||| ||| ||    |||     
-----------------------------------------------------------------gtaatgtggtaccagattgatcacaatt----tttcactcctttggtttcagcctac--tggttatgaacaccactctt-tgccca-tgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

upper sequence: PP1S163_94V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GRMZM2G063851_T05 (Zea mays), 3'ss of exon 3
gtacggtttttttatgtctgtccaccacaataggcctagatattcaatttgaatttaacttgggagtaaaaagcacccagctactcggaataatggttgtagtcacttcatgcaagattgtaacgctcgtgactagtcttccagtgcataattttttgacagGTAAAAAACCCATGGCCGAATGTAGATGCTCATAGTGGAGTATTGCTTCAACACTATGGTCTGAAAGAACAGAA
                                           |   |  ||||||   |      |      || |||     |  |  || |||   ||  |     | ||  | |   |||       |||| ||||   |  |||  ||| |   ||||| || ||||||||||| ||||| |||||||| |||||||| |||||  | |||| ||| ||    |||     
------------------------------------------cttcttaagaatttttttccaatct------catccaatccat--gtgtattgggaataaccgaacaaagcctggtgtgaac-------actattcttt--gcccatgttttct---cagGTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

upper sequence: PP1S163_94V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 17
gtacggtttttttatgtctgtccaccacaataggcctagatattcaatttgaatttaacttgggagtaaaaagcacccagctactcggaataatggttgtagtcacttcatgcaagattgtaacgctcgtgactagt-cttccagtgcataattttttgacagGTAAAAAACCCATGGCCGAATGTAGATGCTCATAGTGGAGTATTGCTTCAACACTATGGTCTGAAAGAACAGAA
                                                                 | || | ||   |    | || | | |||     | |   |||||   |    |||   | |       | |  ||   |    |       |   |||| |||||||||||||| ||||| |||||||| ||||| || |||||  | || | |||| |  | |||     
-------------------------------------------------------------ttctgcaacatgcctactagaattctgtaaaataaactttg--gcttcagtgatacctgtggagttaacagtgattgtttttgggatttgggacacttgtagGTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgcaagattgtaacgctcgtgactagtcttccagtgcataattttttgacagGTAAAAAACCCATGGCCGAATGTAGATGCTCATAGTGGAGTATTGCTTCAACACTATGGTCTGAAAGAACAGAA
          ttgtaac  putative branch site (score: 2)
                                            tttttt  putative PPT
                                        ataattttttgaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggtttttttatgtctgtccaccacaataggcctagatattcaatttgaatttaacttgggagtaaaaagcacccagctactcggaataatggttgtagtcacttcatgcaagattgtaacgctcgtgactagtcttccagtgcataattttttgacagGTAAAAAACCCATGGCCGAATGTAGATGCTCATAGTGGAGTATTGCTTCAACACTATGGTCTGAAAGAACAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC