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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaacgaatcctcgccattcctaacatgatgtctttgaagatgatttcaaattcgtataggacctctcatgaaaagggcaattgtttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTTGAAAGAGACGCTAAGGGAAAGCTCTTGTCTGATGGTACATGGACATACA

Basic information

species Physcomitrella patens
transcript PP1S93_48V6.1
intron # 10
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|162250870|gb|FC426914.1|FC426914
EST:     TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162190070|gb|FC366644.1|FC366644
EST:     ACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: ACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162157103|gb|FC333673.1|FC333673
EST:     TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162186773|gb|FC362809.1|FC362809
EST:     TTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGA-TTGTTTTTGACAGAGGATGT
genomic: TTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTG-TTTTGACAGAGGATGT
EST: gi|162191399|gb|FC367142.1|FC367142
EST:     ACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: ACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162199012|gb|FC375782.1|FC375782
EST:     GTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: GTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|37850055|gb|BJ608063.1|BJ608063
EST:     TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|37848061|gb|BJ606069.1|BJ606069
EST:     TCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: TCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162194329|gb|FC368512.1|FC368512
EST:     AAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: AAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162155923|gb|FC332472.1|FC332472
EST:     ACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: ACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162158927|gb|FC334800.1|FC334800
EST:     AAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATG-T
genomic: AAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162151232|gb|FC327192.1|FC327192
EST:     TAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: TAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|37844012|gb|BJ602020.1|BJ602020
EST:     TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|19781537|gb|BQ039733.1|BQ039733
EST:     TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162221572|gb|FC397589.1|FC397589
EST:     GAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: GAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162152766|gb|FC329772.1|FC329772
EST:     CGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTG-TTTGACAGAGGATGTT
genomic: CGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162191113|gb|FC367375.1|FC367375
EST:     TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162193300|gb|FC370918.1|FC370918
EST:     TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162231672|gb|FC407641.1|FC407641
EST:     ACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATAGGATTTGTTTTGACAGAGGATGTT
genomic: ACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162166947|gb|FC343332.1|FC343332
EST:     TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTG
genomic: TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTG
EST: gi|162152767|gb|FC329773.1|FC329773
EST:     TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|100430081|gb|BY978237.1|BY978237
EST:     TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAAGATGTT
genomic: TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162257124|gb|FC432584.1|FC432584
EST:     ACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: ACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|162154017|gb|FC330252.1|FC330252
EST:     ACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: ACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
EST: gi|37838554|gb|BJ596562.1|BJ596562
EST:     TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAG                         GTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT
genomic: TTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTT

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: 10

GTCGAGGTTAACCTGTTAACAGGGGAAACAAGAATCTTGGCTGTGGATCTTATCTACGACTCTGGAAAAAGTATAAACGTAGCTGTTGATATCGGACAGgtgaacgaat ... ttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTTGAAAGAGACGCTAAGGGAAAGCTCTTGTCTGATGGTACATGGACATACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatttcaaattcgtataggacctctcatgaaaagggcaattgtttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTTGAAAGAGACGCTAAGGGAAAGCTCTTGTCTGATGGTACATGGACATACA
                                         ttgttttt  CT-rich tract
                                       aattgtttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaacgaatcctcgccattcctaacatgatgtctttgaagatgatttcaaattcgtataggacctctcatgaaaagggcaattgtttttatgcagGTAGAGGGTGGCTTCGTGTTTGGTATTGGATTTGTTTTGACAGAGGATGTTGAAAGAGACGCTAAGGGAAAGCTCTTGTCTGATGGTACATGGACATACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA