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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtcttctgattctgtgaagaaagttttccattttttattaagccactcagcatttgtttcaaaattttcaatgacgtttagttgatatcagtcaaatcgtgtaaaacatattggggttttgtttctcatgatcatatcgtaatctaaaaatcgaatttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATCTCTCGGGCTGGGATTGATCAATCACAAGTGGATTTCTATGAAATCAATG

Basic information

species Physcomitrella patens
transcript PP1S160_44V6.1
intron # 9
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|208364951|gb|DC947093.1|DC947093
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|18333054|gb|BJ165068.1|BJ165068
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|208357273|gb|DC949903.1|DC949903
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|208372747|gb|DC952634.1|DC952634
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|67724453|gb|BJ974712.1|BJ974712
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|37824997|gb|BJ583063.1|BJ583063
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|67727140|gb|BJ977399.1|BJ977399
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|37828592|gb|BJ586604.1|BJ586604
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|22132646|gb|BQ827270.1|BQ827270
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|162173639|gb|FC349607.1|FC349607
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|208385682|gb|DC952843.1|DC952843
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|18335246|gb|BJ167264.1|BJ167264
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|162166658|gb|FC343550.1|FC343550
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|208375552|gb|DC945111.1|DC945111
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|37838686|gb|BJ596694.1|BJ596694
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|208362030|gb|DC950479.1|DC950479
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|40781593|gb|AJ583523.1|AJ583523
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|162177571|gb|FC352429.1|FC352429
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|162231216|gb|FC407003.1|FC407003
EST:     ATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: ATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|208389390|gb|DC953228.1|DC953228
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|162177570|gb|FC352428.1|FC352428
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|22492620|gb|BU052543.1|BU052543
EST:     CGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: CGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|208362110|gb|DC943523.1|DC943523
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|67728109|gb|BJ978368.1|BJ978368
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|208367940|gb|DC955375.1|DC955375
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|208353436|gb|DC922490.1|DC922490
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|162258772|gb|FC434571.1|FC434571
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|19782978|gb|BQ039945.1|BQ039945
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|208388349|gb|DC949321.1|DC949321
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
EST: gi|208368091|gb|DC947651.1|DC947651
EST:     TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAG                         GCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC
genomic: TGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATC

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: 31 (upstream exon), 30 (downstream exon)
Score: 12

TGATGGAGCTGCTGCTCTTGTCCTAGTTAGTGGTGCGAAAGCGAAGGAGTTGGGTCTTCAAGTTATCGCAAAGATTCGTGGATATGCTGATGCTGCACAGgttgtcttct ... ttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATCTCTCGGGCTGGGATTGATCAATCACAAGTGGATTTCTATGAAATCAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggggttttgtttctcatgatcatatcgtaatctaaaaatcgaatttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATCTCTCGGGCTGGGATTGATCAATCACAAGTGGATTTCTATGAAATCAATG
                              atctaaa  putative branch site (score: 12)
                                 taaaaatcgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtcttctgattctgtgaagaaagttttccattttttattaagccactcagcatttgtttcaaaattttcaatgacgtttagttgatatcagtcaaatcgtgtaaaacatattggggttttgtttctcatgatcatatcgtaatctaaaaatcgaatttgttggtagGCCCCTGAACTCTTTACGACTTCGCCAGCAATTGCCATTCCTAAAGCAATCTCTCGGGCTGGGATTGATCAATCACAAGTGGATTTCTATGAAATCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA