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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttcgaaggtttaagaactttatgaagtagtcgccgtcaagaaaaaaaattccacttcttttgaagtcattttgaagtcttacttgtgttcgtgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA

Basic information

species Physcomitrella patens
transcript PP1S37_33V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_33V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 17
gtaagtttcgaaggtttaagaactttatgaagtagtcgccgtcaagaaaaaaaattccacttcttttgaagtcattt-tgaagtcttacttgtgttcgtgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA
||||   |   || || |  ||  | || |  | |   |  | |  |       |||   ||  ||  |  |||||    |||   ||      | | |   |   |  ||||||||| ||||| ||||||||||| |||||||||||||| || || ||  |  |||  || ||    |||     
gtaatgctactagattgatcaa--taatta--ttgctcctttaattacggctccttcagtttacttccatctcattggctaagaaataagaacatcctt---cacattttcagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGCGGAGTTCTACTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: PP1S37_33V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 17
gtaagtttcgaaggtttaagaactttatgaagtagtcgccgtcaag--aaaaaaaattccacttcttttgaagtcattttgaagtcttacttgtgttcg---tgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA
                               ||| | |||   |     |  |  ||| |     ||||     ||| ||   | || |   |||       ||| |   |   |||||||| ||||| ||||||||||| ||||||||||| || || |||||  |  |||  || ||    |||     
-------------------------------gtaat-gccactagattgatcatgattgctaccgttttatgtccatcttattggctaaaaagtgacaacattgtccatatttccagGTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCG

upper sequence: PP1S37_33V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 18
gtaagtttcgaaggtttaagaactttatgaagtagtcgccgtcaagaaaaaaaattccacttcttttgaagtcattttgaagtctt----acttgtgttcgtgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA
                           | | || ||  | |       | ||  || |||| |||| |        |    ||  |    ||   | || |     |  |  ||||||||||||||| ||||| ||||| ||||||||||| || ||  ||||  |  |||  ||  |    |||     
--------------------------gtaatgtggtaccagattgatcacaatttttcactcctttggtttcagcctactggttatgaacaccactctttgcccatgttttctcagGTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

upper sequence: PP1S37_33V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G063851_T05 (Zea mays), 3'ss of exon 3
gtaagtttcgaaggtttaagaactttatgaagtagtcgccgtcaagaaaaaaaattccacttcttttgaagtcattttgaagtct-tacttgtgttcgtgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA
               ||||||| ||| |     | || |   |||   |      |           |||   |   ||  ||    |||  | || |     |  |  ||||||||||||||| ||||| ||||| ||||||||||| || ||  ||||  |  |||  ||  |    |||     
-----------cttcttaagaatttttttc--caatctcatccaatccatgtgtattgggaataaccgaacaaagcctggtgtgaacactattctttgcccatgttttctcagGTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG

upper sequence: PP1S37_33V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 16
gtaagtttcgaaggtttaagaactttatgaagtagtcgccgtcaagaaaaaaaattccacttcttttgaagtcattttgaagtcttacttgtgttcgtgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA
                         ||  |  ||  | |  |||    |     | |||  | || |||  |  | |    || |||    | ||    |    || |||||||||||||||| |||||||| || |||||||| ||||| || || ||  | ||||| ||  | |  |||   | 
------------------------gtactacttatactcattcatttcatgtgctaccagattttctgattttctct---ggttttatgaatcttgaaattgctgt-atcagGTCAAGAACCCGTGGCCTAACGTTGATGCTCATAGCGGAGTGCTTCTGAACTACTATGGTCTAACCGAAGCAAG

upper sequence: PP1S37_33V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: EDO96721 (Chlamydomonas reinhardtii), 3'ss of exon 11
gtaagtttcgaaggtttaagaactttatgaagtagtcgccgtcaagaaaaaaaattccacttcttttgaagtcattttgaagtcttacttgtgttcgtgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA--------------------------
    |  | |   ||       | |||| |   |  |||   |      |     | | |  ||  ||||  |        ||||    ||  | ||  |||        || |||||||||||||||| || ||||| || |||||||| || ||||| |||||||||||| | |  ||  ||||                          
-acggccttgcctgtcctgccgccttatca--cacccgcttcccgcgccaccgcctgctcc-ctcctgaaccctgcccctggtctccgctgcttgcggctgc--------agATCAAGAACCCCTGGCCCAACGTGGACGCGCACAGCGGCGTGCTGCTGCAGTACTACGGCATCACGGAGGAGAACTACTACACGGTGCTGTTCGGGGTGT

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|162176172|gb|FC351914.1|FC351914
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|162165708|gb|FC340889.1|FC340889
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|208386538|gb|DC952747.1|DC952747
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|67697462|gb|BJ957695.1|BJ957695
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|37823157|gb|BJ581223.1|BJ581223
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|208388659|gb|DC953435.1|DC953435
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|208363044|gb|DC957985.1|DC957985
EST:     TATCGAAATNGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|37847922|gb|BJ605930.1|BJ605930
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|37835509|gb|BJ593521.1|BJ593521
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|162152561|gb|FC328839.1|FC328839
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|67724660|gb|BJ974919.1|BJ974919
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|162194037|gb|FC370212.1|FC370212
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|208356950|gb|DC922286.1|DC922286
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|162234310|gb|FC409848.1|FC409848
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|37825198|gb|BJ583264.1|BJ583264
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
EST: gi|162202112|gb|FC378033.1|FC378033
EST:     TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAG                         GTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG
genomic: TATCGAAATTGTTTGAGGTGGTTCCTCCTATTCTTTTGGCAGGCGGAAAGgtaagtttcg ... gagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttcttttgaagtcattttgaagtcttacttgtgttcgtgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA
                        gtcttac  putative branch site (score: 3)
                attttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttcgaaggtttaagaactttatgaagtagtcgccgtcaagaaaaaaaattccacttcttttgaagtcattttgaagtcttacttgtgttcgtgtgcgagtgatcagGTCAAGAACCCCTGGCCTAATGTGGATGCTCACAGCGGTGTCCTGCTTCAGTACTACGGCTTGAAAGAACAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC