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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgcgctgtttattgatgtttaccatgttaagtgtgtttggttgcaatgtcgctgctactctacagttcttagaccctgttgattttccctgaactgtgtgtgccgttgagattgcagATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTCCGAGTGATGCAGTTCTTGAAATCGAGCTTGAGCTCATTTCATGGAAAGT

Basic information

species Physcomitrella patens
transcript PP1S109_70V6.1
intron # 6
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|162221593|gb|FC397610.1|FC397610
EST:     GAAGACTATGTTAAAAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGAT                         ATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTC
genomic: GAAGACTATGTTAAAAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGATgtaagtgcgc ... gagattgcagATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTC
EST: gi|162160213|gb|FC337110.1|FC337110
EST:     GAAGACTATGTTAAAAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGAT                         ATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTC
genomic: GAAGACTATGTTAAAAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGATgtaagtgcgc ... gagattgcagATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTC
EST: gi|162173905|gb|FC349705.1|FC349705
EST:     GAAGACTATGTTAAAAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGAT                         ATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTC
genomic: GAAGACTATGTTAAAAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGATgtaagtgcgc ... gagattgcagATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTC
EST: gi|100435874|gb|BY979267.1|BY979267
EST:     ATGTTAAAAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGAT                         ATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTC
genomic: ATGTTAAAAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGATgtaagtgcgc ... gagattgcagATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTC
EST: gi|162193217|gb|FC371524.1|FC371524
EST:     GAAGACTATGTTAAAAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGAT                         ATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTC
genomic: GAAGACTATGTTAAAAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGATgtaagtgcgc ... gagattgcagATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTC
EST: gi|162172470|gb|FC349139.1|FC349139
EST:     GAAGACTATGTTAACAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGAT                         ATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTAT
genomic: GAAGACTATGTTAAAAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGATgtaagtgcgc ... gagattgcagATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTAT

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: 78

GGCATTTCTGTCCTGCGATTGGCCAGGCAGTGAAGACTATGTTAAAAGGAGAGAAAGCACTACTGACAGTGAAGCCCCGATgtaagtgcgc ... gagattgcagATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTCCGAGTGATGCAGTTCTTGAAATCGAGCTTGAGCTCATTTCATGGAAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttcttagaccctgttgattttccctgaactgtgtgtgccgttgagattgcagATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTCCGAGTGATGCAGTTCTTGAAATCGAGCTTGAGCTCATTTCATGGAAAGT
              tgttgat  putative branch site (score: 78)
                ttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgcgctgtttattgatgtttaccatgttaagtgtgtttggttgcaatgtcgctgctactctacagttcttagaccctgttgattttccctgaactgtgtgtgccgttgagattgcagATGGATTTGGAGAGAAGGGAGCAGCTCCCTCTGGAGATGTGAAAGCTATTCCGAGTGATGCAGTTCTTGAAATCGAGCTTGAGCTCATTTCATGGAAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA