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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGCTTGAAGCATTATTGAATGCAGTCAACAATGGTGATAATAGCCACATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgggttttccacagtttactctcgacgggttgagtttgtaatttacaggttttaagttattggggatctattccagtgtttcaagcaagctcg...

Basic information

species Physcomitrella patens
transcript PP1S14_318V6.1
intron # 5
splice site 5'
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|100381151|gb|BY950004.1|BY950004
EST:     TCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACNGTAT-GATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAANGTGGAAGTGGATTTGCTGCAGC
genomic: TCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGAC-GTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|100410542|gb|BY992154.1|BY992154
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|162235944|gb|FC411687.1|FC411687
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|67719536|gb|BJ969795.1|BJ969795
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAA
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAA
EST: gi|162159573|gb|FC335751.1|FC335751
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|100399854|gb|BY990655.1|BY990655
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAANGTGGAAGTGGATTTGCTGCAGC
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|162270585|gb|FC446510.1|FC446510
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|100361055|gb|BY946891.1|BY946891
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|100444272|gb|BY982301.1|BY982301
EST:     TCGTACATATTCCANGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAACGTAGGCAGTGGATTT
genomic: TCGTACATATTCCA-GGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGT-GGAAGTGGATTT
EST: gi|100426210|gb|BY958783.1|BY958783
EST:     ATCGTACATATTCCAGGAGGAGAAAGAATACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|100410928|gb|BY956252.1|BY956252
EST:     TCGTACATATTCCAGGGAG-AGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTT
genomic: TCGTACATATTCCAGG-AGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTT
EST: gi|100449851|gb|CJ973968.1|CJ973968
EST:     ATCGTACATATTCCAGGAGGAGAA-GAGTACTTNCTGACGTATTGATCAG                         TTCTTCTATCTTNACTGGTGATGGA
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGA
EST: gi|67569334|gb|BJ942158.1|BJ942158
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|208361374|gb|DC930371.1|DC930371
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTG
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTG
EST: gi|100436137|gb|BY979398.1|BY979398
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTANTGATCAG                         TTCTTCTATCTTTACTGG
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGG
EST: gi|162195399|gb|FC370868.1|FC370868
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
EST: gi|67716301|gb|BJ966561.1|BJ966561
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAG                         TTCTTCTATCTT
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTT
EST: gi|100400831|gb|BY972965.1|BY972965
EST:     ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGGATTGATCAG                         TTCTTCTATCTTTACTGGGGATGGAG
genomic: ATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAG
EST: gi|100381386|gb|BY950102.1|BY950102
EST:     CGTACATATTCCCAG-AGGAGAAAGAGTACTTTTCTGACGTAT-GATCAG                         TTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC
genomic: CGTACATATTCC-AGGAGGAGAAAGAGTACTTT-CTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGC

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: 30 (upstream exon), 33 (downstream exon)
Score: 9

AAAAGCTTGAAGCATTATTGAATGCAGTCAACAATGGTGATAATAGCCACATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgg ... ctccacgcagTTCTTCTATCTTTACTGGTGATGGAGAAGGTGGAAGTGGATTTGCTGCAGCTGCTGCCGCATCTGCTGCCGCGGCTGCCGTTGGTGGTGGAGGTGGTGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAGCTTGAAGCATTATTGAATGCAGTCAACAATGGTGATAATAGCCACATCGTACATATTCCAGGAGGAGAAAGAGTACTTTCTGACGTATTGATCAGgtaaaattgggttttccacagtttactctcgacgggttgagtttgtaatttacaggttttaagttattggggatctattccagtgtttcaagcaagctcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA