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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtcttctctctgggacagacataggtcaatacaaaatatctatcatacataacatatgttctgttattcatctgtaggaatcacgattcgtcgacaagttcaattctcttctacagggtttctgatttgaatctttccgttttttggaaactgctttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAACAATCATTATGTTCTATTACCCATCCCAGAGGTGATTGCCTACGCAAGAA

Basic information

species Physcomitrella patens
transcript PP1S94_106V6.1
intron # 12
splice site 3'
intron type U2

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|67693514|gb|BJ953747.1|BJ953747
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|162203811|gb|FC379908.1|FC379908
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|37852524|gb|BJ610532.1|BJ610532
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|7648346|gb|AW739329.1|AW739329
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|18336359|gb|BJ168381.1|BJ168381
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACCTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|162229043|gb|FC404753.1|FC404753
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|67697835|gb|BJ958068.1|BJ958068
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|162198099|gb|FC372126.1|FC372126
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|37824275|gb|BJ582341.1|BJ582341
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|37850516|gb|BJ608524.1|BJ608524
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|7648257|gb|AW739240.1|AW739240
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
EST: gi|162229044|gb|FC404754.1|FC404754
EST:     GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCG                         GTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC
genomic: GAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAAC

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: 27 (upstream exon), 35 (downstream exon)
Score: 7

AGCAGCGGATGTGAAGTACATCGATCCTACGTACATGATCCGAGCCTGTCGAGCTAATGCTTCTGACCGAATCTTGTGTGCTGTACTTGGGCAGAACGCGgtatgtcttc ... ttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAACAATCATTATGTTCTATTACCCATCCCAGAGGTGATTGCCTACGCAAGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacagggtttctgatttgaatctttccgttttttggaaactgctttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAACAATCATTATGTTCTATTACCCATCCCAGAGGTGATTGCCTACGCAAGAA
         ttctgat  putative branch site (score: 7)
                                        ctgcttt  putative PPT
              atttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtcttctctctgggacagacataggtcaatacaaaatatctatcatacataacatatgttctgttattcatctgtaggaatcacgattcgtcgacaagttcaattctcttctacagggtttctgatttgaatctttccgttttttggaaactgctttgtatacagGTGCATGCTGGTTTTGCTGGATTCACCGGTGTTACTGTTGGAATCGCAAACAATCATTATGTTCTATTACCCATCCCAGAGGTGATTGCCTACGCAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA