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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcataattttttcgtgatgtttttctctaagtatcttgtctaaacttgaaactcgtagtgaggaaaatatgggttctttttgatctactcgcatggcagcttgctgatgctcaattgtttgtgtcacaaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGAAGCTGCCCTTGAGGCGTACTCGAAGTCATACCCCGAAGAGGCTGCAGAG

Basic information

species Physcomitrella patens
transcript PP1S72_25V6.1
intron # 5
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|162187677|gb|FC364628.1|FC364628
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162166276|gb|FC342869.1|FC342869
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162241293|gb|FC416924.1|FC416924
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162258554|gb|FC434769.1|FC434769
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162162334|gb|FC339130.1|FC339130
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162272679|gb|FC448305.1|FC448305
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162151356|gb|FC327485.1|FC327485
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162173575|gb|FC350149.1|FC350149
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162155491|gb|FC330974.1|FC330974
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162154792|gb|FC331106.1|FC331106
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162153909|gb|FC329416.1|FC329416
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162231766|gb|FC408528.1|FC408528
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162157000|gb|FC333362.1|FC333362
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162186385|gb|FC362941.1|FC362941
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162160705|gb|FC337228.1|FC337228
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162193953|gb|FC371766.1|FC371766
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162166482|gb|FC343179.1|FC343179
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162254172|gb|FC429696.1|FC429696
EST:     AGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162181534|gb|FC358148.1|FC358148
EST:     GCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: GCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162195116|gb|FC368804.1|FC368804
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162268645|gb|FC443699.1|FC443699
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162248959|gb|FC421458.1|FC421458
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162160911|gb|FC337468.1|FC337468
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162193760|gb|FC368700.1|FC368700
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162174042|gb|FC350557.1|FC350557
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162180307|gb|FC355312.1|FC355312
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162190600|gb|FC366238.1|FC366238
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162196635|gb|FC374925.1|FC374925
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162254948|gb|FC431133.1|FC431133
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162176957|gb|FC353634.1|FC353634
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162161260|gb|FC337323.1|FC337323
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162185533|gb|FC361257.1|FC361257
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162177841|gb|FC355091.1|FC355091
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162173510|gb|FC350084.1|FC350084
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
EST: gi|162167290|gb|FC342278.1|FC342278
EST:     AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAG                         TCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA
genomic: AACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGA

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: 35 (upstream exon), 34 (downstream exon)
Score: 98

CTGTGCATGGTGCCGCTCTGGGAACAAAAGAAGTAGATGCAACCCGCCAAAACCTTAAATGGGACCATGAGCCTTTCTTCGTTCCCGAGGAGGTCAAGAGgtgcataatt ... aaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGAAGCTGCCCTTGAGGCGTACTCGAAGTCATACCCCGAAGAGGCTGCAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctactcgcatggcagcttgctgatgctcaattgtttgtgtcacaaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGAAGCTGCCCTTGAGGCGTACTCGAAGTCATACCCCGAAGAGGCTGCAGAG
                   tgctgat  putative branch site (score: 98)
                              aattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcataattttttcgtgatgtttttctctaagtatcttgtctaaacttgaaactcgtagtgaggaaaatatgggttctttttgatctactcgcatggcagcttgctgatgctcaattgtttgtgtcacaaatgaacagTCACTGGAGCAAGCACATCGATCTTGGATCCAAGCTGGAATCTGACTGGGAAGCTGCCCTTGAGGCGTACTCGAAGTCATACCCCGAAGAGGCTGCAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG