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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggatagaaatgcgcgtctatcaatttaacaggcccgaatgagagcttctgtattcaattttgggcttgtcctaatattcgacagtgaacgtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTGCTGCTAAGAAAGCAGGGAAAGCTCCTGACGTCTTCTATTGCTTGCGGCT

Basic information

species Physcomitrella patens
transcript PP1S215_28V6.1
intron # 11
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|162186161|gb|FC361365.1|FC361365
EST:     GTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162177268|gb|FC353425.1|FC353425
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162151905|gb|FC328151.1|FC328151
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162153917|gb|FC329424.1|FC329424
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162267037|gb|FC441838.1|FC441838
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162217936|gb|FC393932.1|FC393932
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162186626|gb|FC363598.1|FC363598
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|37824967|gb|BJ583033.1|BJ583033
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162178884|gb|FC354816.1|FC354816
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162186047|gb|FC361875.1|FC361875
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162207831|gb|FC384124.1|FC384124
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162178100|gb|FC354402.1|FC354402
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162177755|gb|FC354589.1|FC354589
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162188179|gb|FC363945.1|FC363945
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162269856|gb|FC445386.1|FC445386
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162214586|gb|FC390617.1|FC390617
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162178885|gb|FC354817.1|FC354817
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162176653|gb|FC352498.1|FC352498
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162188180|gb|FC363946.1|FC363946
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162179082|gb|FC356483.1|FC356483
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162186162|gb|FC361366.1|FC361366
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTT
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTT
EST: gi|162184663|gb|FC361901.1|FC361901
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162189252|gb|FC366748.1|FC366748
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162189251|gb|FC366747.1|FC366747
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTNTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162253479|gb|FC430113.1|FC430113
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162269857|gb|FC445387.1|FC445387
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTG
EST: gi|162253480|gb|FC430114.1|FC430114
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162217937|gb|FC393933.1|FC393933
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|37825494|gb|BJ583560.1|BJ583560
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162166510|gb|FC343207.1|FC343207
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATNGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162151637|gb|FC327766.1|FC327766
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162155909|gb|FC332458.1|FC332458
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162181981|gb|FC356852.1|FC356852
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAACTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|208376494|gb|DC922525.1|DC922525
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG
EST: gi|162267038|gb|FC441839.1|FC441839
EST:     GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGG                         GAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAAGCTGCTATTGCTG
genomic: GACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTG

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: 34 (upstream exon), 35 (downstream exon)
Score: 29

TGAAGCTATCTCGCTGTCTTTGAGGAAAAGAGCGCATATCATGACAGATGGTTTCAATGCTTGTGAAAACATTGTCTGCAATTTTACGGAGGgtaatgaatt ... gtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTGCTGCTAAGAAAGCAGGGAAAGCTCCTGACGTCTTCTATTGCTTGCGGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctgtattcaattttgggcttgtcctaatattcgacagtgaacgtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTGCTGCTAAGAAAGCAGGGAAAGCTCCTGACGTCTTCTATTGCTTGCGGCT
                        tcctaat  putative branch site (score: 29)
      tattcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggatagaaatgcgcgtctatcaatttaacaggcccgaatgagagcttctgtattcaattttgggcttgtcctaatattcgacagtgaacgtggttgcagGAGCCATGTACTCTTTCCCACAAGTAAAGTTGCCCCAGGCTGCTATTGCTGCTGCTAAGAAAGCAGGGAAAGCTCCTGACGTCTTCTATTGCTTGCGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA