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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttcgggtctttctgtttgttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatcaaggtcgtgtcttgttccaatagtttcaccagTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGA

Basic information

species Physcomitrella patens
transcript PP1S56_243V6.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AC230013.2_FGT007 (Zea mays), 3'ss of exon 1
ttttcgggtctttctgttt-gttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatcaaggtcgtgtctt-gttccaat--agtttcaccagTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGA
  |  |  |  | ||| |  || ||||  |  | | |||       | |||   |  |||    ||||  ||  | ||  || |  ||  |  |||| || |||||||||||||| ||||| || ||||| ||  ||  | | |||  ||| |||   |||||||||||||| |||||||| |||||||| ||||         
-gtgagtcttctcctgctccgtccatc-cgactgcggtgattagaatttga---tccatgggtttgatttagcccctgctttcgcacctgtgcagTTCCATCAGTACCAGGTGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCG---------

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G022619_T02 (Zea mays), 3'ss of exon 1
------------------------ttttcgggtctttctgttt--gttcatcatggtttcagtgtactt--tttctgaaatttgatgatgctgatcaaggtcgtgtcttgttccaatagtttcaccagTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGA
                          | |   ||||  ||| |   | |  |  |  ||   | | |    | | |   || |      |||  ||       |||  || | |   |||| || |||||||||||||| || || || ||||| ||  | ||| |||||  ||| |||   |||||||||||||| |||||||||||||| || ||||         
gtaagcctaccgccgccgccgcctcctccatctcttcttgtcttgatccgacgcgtcttttctctccccggtgtttctgatctc-caccgcttttctgttatatgttctggtgcggcagTTCCATCAGTACCAGGTGGTGGGTCGCGCGCTGCCGACCCCGACCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACTAACGAGGTTCGCG---------

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv19s0135g00100.t01 (Vitis vinifera), 3'ss of exon 1
--------ttttcgggtctttctgtttgttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatc--aaggtcgtgtcttgttccaatagtttcaccagTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGA
        ||   |  | ||   |       | ||  |    || ||  ||| | | |    |||   |  ||||    |  | |  || | |      |||||||||||||||||||||||||| ||||||| ||  | |   |  |||||   |||| |   ||| | |||||||| ||||| || ||||| || || |         
tttttcttttcctgaattttctcggcaaccaaacaaaggaatag-gtgttttatttaattcctgaatctattgattctgaaatgggttcgtttgggcgcagTTTCACCAGTACCAGGTGGTAGGGAGGGCCCTTCCTTCGGAATCGGATGAGCATCCGAGGATCTACAGGATGAAGCTTTGGGCTACGAACGAGGTTCGTG---------

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|18346144|gb|BJ178187.1|BJ178187
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|162235022|gb|FC411809.1|FC411809
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|67719554|gb|BJ969813.1|BJ969813
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|18367074|gb|BJ199154.1|BJ199154
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|208353060|gb|DC926083.1|DC926083
EST:     CATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: CATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|162206290|gb|FC382568.1|FC382568
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|18372508|gb|BJ204110.1|BJ204110
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|162260389|gb|FC436068.1|FC436068
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGG                         TACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAG
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gtttcaccagTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAG
EST: gi|67726640|gb|BJ976899.1|BJ976899
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|37852027|gb|BJ610035.1|BJ610035
EST:     TCTCGGGGATTCCTGTACACCGCCATGAGCTTCGGTTTCACCAG                         TACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAA
genomic: TCTCGGGGATTCCTGTACACCGCCATGAG---C--TTT---CGGgtgcgtactt ... gtttcaccagTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAA
EST: gi|208398326|gb|DC912311.1|DC912311
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|19780393|gb|BQ039555.1|BQ039555
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|208375525|gb|DC940523.1|DC940523
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|162270822|gb|FC446851.1|FC446851
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|19790807|gb|BQ042066.1|BQ042066
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|67727824|gb|BJ978083.1|BJ978083
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|208391446|gb|DC937594.1|DC937594
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|67718152|gb|BJ968411.1|BJ968411
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|208394496|gb|DC953535.1|DC953535
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|18325024|gb|BJ157020.1|BJ157020
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|18366391|gb|BJ198470.1|BJ198470
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|7067340|gb|AW497195.1|AW497195
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|18360441|gb|BJ192503.1|BJ192503
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|37825253|gb|BJ583319.1|BJ583319
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt
EST: gi|162264738|gb|FC440305.1|FC440305
EST:     TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGTTTCACCAG                 
genomic: TACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTC-G--------Ggtgcgtactt ... gt

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 2

CAGTGTGCGTCGGGGGTGTGGTTGGGAGGAAGGGCAGGCTGTCGCCCCGTTACCCTGCTTCGCATCTCGGGGATTCCTGTACACCGCCATGAGCTTTCGGgtgcgtactt ... gtttcaccagTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgaaatttgatgatgctgatcaaggtcgtgtcttgttccaatagtttcaccagTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGA
               tgctgat  putative branch site (score: 2)
                                              tttcacc  putative PPT
     aatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcgggtctttctgtttgttcatcatggtttcagtgtactttttctgaaatttgatgatgctgatcaaggtcgtgtcttgttccaatagtttcaccagTACCAGGTGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC