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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTGTCCTACGATCCGAATCTTCGGCTGCCCTTGTGGCCGTCGGCTGACGCCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgtttttttttcattgctctcgtacacatctttgtttggtgtgatagcatgaaaatttgtagccctattccaaggctctcatgtacagggagtattgctctcattgagcaaggtgatcaaggaaaatgtcgatggtttctaagcgaagctcaacacagagataaattctgcgacatggtttgttgtgcag

Basic information

species Physcomitrella patens
transcript PP1S127_105V6.1
intron # 4
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|162255602|gb|FC431600.1|FC431600
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|162159123|gb|FC334294.1|FC334294
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|18335485|gb|BJ167505.1|BJ167505
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|18340869|gb|BJ172900.1|BJ172900
EST:     CCGCGAAGNAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|18339396|gb|BJ171423.1|BJ171423
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|208396708|gb|DC920388.1|DC920388
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GCCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|162193816|gb|FC371291.1|FC371291
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|6102356|gb|AW126826.1|AW126826
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACAANGAGGTTATATTTCTAACTGGTGCCGACCCC
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCC
EST: gi|162255603|gb|FC431601.1|FC431601
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|162159124|gb|FC334295.1|FC334295
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|67724820|gb|BJ975079.1|BJ975079
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|162197072|gb|FC372450.1|FC372450
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|162263645|gb|FC438881.1|FC438881
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|162197071|gb|FC372449.1|FC372449
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|208386135|gb|DC949046.1|DC949046
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|6102385|gb|AW126855.1|AW126855
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|162280370|gb|FC456075.1|FC456075
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|162263646|gb|FC438882.1|FC438882
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|162193789|gb|FC371290.1|FC371290
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
EST: gi|162280371|gb|FC456076.1|FC456076
EST:     CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAG                         GTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT
genomic: CCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGAT

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: 33 (upstream exon), 34 (downstream exon)
Score: 12

CCTGTCCTACGATCCGAATCTTCGGCTGCCCTTGTGGCCGTCGGCTGACGCCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgttttttttt ... tgttgtgcagGTCAGTGACGAGGAGGTTATATTTCTTACTGGTGCCGACCCCAAGGATGATGCACACAACCTGAAAATGATGCCCGCTGGCTGCAGGTTGATGCTAGTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTGTCCTACGATCCGAATCTTCGGCTGCCCTTGTGGCCGTCGGCTGACGCCGCGAAGGAAGGCATTATGTCGATTTGGGATCAGGCCGATATCATAAAGgtttttttttcattgctctcgtacacatctttgtttggtgtgatagcatgaaaatttgtagccctattccaaggctctcatgtacagggagtattgctctcattgagcaaggtgatcaaggaaaatgtcgatggtttctaagcgaagctcaacacagagataaattctgcgacatggtttgttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA