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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacttgataagtaatttgaggttttgttactcctagctgtacaagtttcttgcacatgggtcattcagtcattgattctaactcgttcttctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAAGGATGACAAGGAGGCCATGCCTGGCATGGGAGGTGGAATGGGAGGAATG

Basic information

species Physcomitrella patens
transcript PP1S149_289V6.1
intron # 16
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|162159174|gb|FC334345.1|FC334345
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|162198558|gb|FC373404.1|FC373404
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|208356851|gb|DC926862.1|DC926862
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|162192962|gb|FC371945.1|FC371945
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|162175003|gb|FC350902.1|FC350902
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|162156171|gb|FC332546.1|FC332546
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|162192963|gb|FC371946.1|FC371946
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGA-
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|37838395|gb|BJ596403.1|BJ596403
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|67696511|gb|BJ956744.1|BJ956744
EST:     GATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: GATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|162175002|gb|FC350901.1|FC350901
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|37850096|gb|BJ608104.1|BJ608104
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|162268426|gb|FC444195.1|FC444195
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|162234666|gb|FC410412.1|FC410412
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|208369434|gb|DC955895.1|DC955895
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|162276484|gb|FC452682.1|FC452682
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|162156170|gb|FC332545.1|FC332545
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|162183371|gb|FC359286.1|FC359286
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|162268425|gb|FC444194.1|FC444194
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
EST: gi|208366302|gb|DC947546.1|DC947546
EST:     ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAG                         CGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA
genomic: ATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAA

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: 19 (upstream exon), 20 (downstream exon)
Score: 3

CCGAGTACGTCGACATGGTGAAGGCTGGAATTATTGATCCTGTAAAGGTTATTAGAACAGCTCTTGTTGATGCCGCTAGgtactttttt ... ctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAAGGATGACAAGGAGGCCATGCCTGGCATGGGAGGTGGAATGGGAGGAATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttgcacatgggtcattcagtcattgattctaactcgttcttctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAAGGATGACAAGGAGGCCATGCCTGGCATGGGAGGTGGAATGGGAGGAATG
                              ttctaac  putative branch site (score: 3)
                                    ctcgttcttct  CT-rich tract
                         attgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacttgataagtaatttgaggttttgttactcctagctgtacaagtttcttgcacatgggtcattcagtcattgattctaactcgttcttctgtgtgcagCGTTGCATCACTGATGACAACAACTGAAGCAGTAATTGCTGATTTCCCGAAGGATGACAAGGAGGCCATGCCTGGCATGGGAGGTGGAATGGGAGGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - ctgtaca
- - - - - - - - - - - - - - - - - - - - - - - - - - cacatgg