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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttcatcactttcagcctggctactgagagaattgctttattttaactatagaaattcatgcgggtaatgatgtgctgtgcatctcatgtatctgatagGTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCG

Basic information

species Physcomitrella patens
transcript PP1S37_304V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G011518_T04 (Zea mays), 3'ss of exon 1
-ctttcatcactttcagcctggctactgagagaattgctttattttaactatagaaattcatgcgggtaatgatgtgctgtgcatctcatgtatctgat-agGTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCG---------
   || |    | |     |   |  |  |||| | |    | | |   | |  |  |  |   |  |  | ||    || || ||| || | | |  | |||||||||||||||| ||||| || || || ||||||||||| ||||||||||| || ||||| ||  || | ||||| ||||| ||||| |         
atgtttagtcttctttttttatatcatcggagattagaaccagtatccgttttaagctgaacatgcctc-taatagattg-gcctcttatttttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAGGTCCGATTG

upper sequence: PP1S37_304V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G011518_T03 (Zea mays), 3'ss of exon 1
-ctttcatcactttcagcctggctactgagagaattgctttattttaactatagaaattcatgcgggtaatgatgtgctgtgcatctcatgtatctgat-agGTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCG
   || |    | |     |   |  |  |||| | |    | | |   | |  |  |  |   |  |  | ||    || || ||| || | | |  | |||||||||||||||| ||||| || || || ||||||||||| ||||||||||| || ||||| ||  || | ||||| ||||| ||||| |
atgtttagtcttctttttttatatcatcggagattagaaccagtatccgttttaagctgaacatgcctc-taatagattg-gcctcttatttttttcctcagGTGGTGATGCTTGGGTTGGATGCAGCTGGGAAAACCACCATACTCTATAAGCTTCACATTGGTGAAGTTCTCTCCACTGTCCCTACCATAG
















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|100449182|gb|CJ973481.1|CJ973481
EST:     ATACCTTCCGCAAGCTCTTTGATTCTATCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTG
genomic: ATACCTTCCGCAAGCTCTTTGATTCTATCTTCGGCAACAAGGAGATGCGGgtacgccaat ... tatctgatagGTGGTGATGCTTG
EST: gi|100394467|gb|BY972083.1|BY972083
EST:     ATACCTTCCGCAAGCTCTTTGATTCTATCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAG
genomic: ATACCTTCCGCAAGCTCTTTGATTCTATCTTCGGCAACAAGGAGATGCGGgtacgccaat ... tatctgatagGTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAG
EST: gi|208360587|gb|DC930859.1|DC930859
EST:     ATACCTTCCGCAAGCTCTTTGATTCTATCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAG
genomic: ATACCTTCCGCAAGCTCTTTGATTCTATCTTCGGCAACAAGGAGATGCGGgtacgccaat ... tatctgatagGTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAG
EST: gi|18362447|gb|BJ194517.1|BJ194517
EST:     ATACCTTCCGCAAGCTCTTTGATTCTATCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAG
genomic: ATACCTTCCGCAAGCTCTTTGATTCTATCTTCGGCAACAAGGAGATGCGGgtacgccaat ... tatctgatagGTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAG
EST: gi|18365645|gb|BJ197722.1|BJ197722
EST:     ATACCTTCCGCAAGCTCTTTGATTCTATCTTCGGCAACAAGGAGATGCGG                         GTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAG
genomic: ATACCTTCCGCAAGCTCTTTGATTCTATCTTCGGCAACAAGGAGATGCGGgtacgccaat ... tatctgatagGTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAG

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), 33 (downstream exon)
Score: 11

CAGTCCAGAGTAGGGATTGCTAGGTTAAGGTGAGCTTGAAGCTATGGGGAATACCTTCCGCAAGCTCTTTGATTCTATCTTCGGCAACAAGGAGATGCGGgtacgccaat ... tatctgatagGTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactatagaaattcatgcgggtaatgatgtgctgtgcatctcatgtatctgatagGTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCG
 ttttaac  putative branch site (score: 11)
     tagaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttcatcactttcagcctggctactgagagaattgctttattttaactatagaaattcatgcgggtaatgatgtgctgtgcatctcatgtatctgatagGTGGTGATGCTTGGATTGGACGCGGCAGGCAAAACCACCATTCTCTATAAGCTGCATATTGGAGAGATTTTGTCCACAGTCCCCACCATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA