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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgatttgcctacgatgatttgcgcttattagttgaggatgcggccatgaggttttgtgacaccctacgatttcagaaattggaagtatccaagtgctggtttgtggatgtcgtgtggacgagtaagcagtcgtttggttatgtaactaattagctttcattgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTCGTGGTGGACAGCAACGATAGAGATCGTGTTGTGGAAGCAAGAGATGAAC

Basic information

species Physcomitrella patens
transcript PP1S70_133V6.1
intron # 2
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|162277024|gb|FC453746.1|FC453746
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|15326959|gb|BI487404.1|BI487404
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|208352568|gb|DC918277.1|DC918277
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|18357424|gb|BJ189483.1|BJ189483
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|67571176|gb|BJ944000.1|BJ944000
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|67702836|gb|BJ963069.1|BJ963069
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAG
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAG
EST: gi|37853120|gb|BJ611128.1|BJ611128
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|100408057|gb|BY955888.1|BY955888
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|37836789|gb|BJ594797.1|BJ594797
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|67694492|gb|BJ954725.1|BJ954725
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|67718998|gb|BJ969257.1|BJ969257
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|162228172|gb|FC404888.1|FC404888
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|37826457|gb|BJ584469.1|BJ584469
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|37844416|gb|BJ602424.1|BJ602424
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|162225288|gb|FC402054.1|FC402054
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|162228171|gb|FC404887.1|FC404887
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|162238040|gb|FC418676.1|FC418676
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|162266235|gb|FC442167.1|FC442167
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|162277025|gb|FC453747.1|FC453747
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|208372537|gb|DC940798.1|DC940798
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|208354370|gb|DC953804.1|DC953804
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|67727335|gb|BJ977594.1|BJ977594
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|162266236|gb|FC442168.1|FC442168
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
EST: gi|162225287|gb|FC402053.1|FC402053
EST:     AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAG                         ATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC
genomic: AATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTC

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), 33 (downstream exon)
Score: 40

GGTTCAATGTGGAGACCGTTGAATACAAGAACATCAGTTTCACCGTTTGGGATGTCGGAGGTCAGGACAAGgtacgatttg ... tgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTCGTGGTGGACAGCAACGATAGAGATCGTGTTGTGGAAGCAAGAGATGAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggacgagtaagcagtcgtttggttatgtaactaattagctttcattgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTCGTGGTGGACAGCAACGATAGAGATCGTGTTGTGGAAGCAAGAGATGAAC
                            aactaat  putative branch site (score: 40)
                                      ctttcatt  putative PPT
                      ttatgtaactaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgatttgcctacgatgatttgcgcttattagttgaggatgcggccatgaggttttgtgacaccctacgatttcagaaattggaagtatccaagtgctggtttgtggatgtcgtgtggacgagtaagcagtcgtttggttatgtaactaattagctttcattgtttcacagATCCGACCATTGTGGAGGCACTATTTCCAGAACACTCAGGGGTTGATCTTCGTGGTGGACAGCAACGATAGAGATCGTGTTGTGGAAGCAAGAGATGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG