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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGATACCGCTGGTCAGGAGAGGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaataatccggatacgtttgtgcacgtggttgtctgttgcatctaacacctctctggatggggctgagtttgattcaattcttaggacttgactg...

Basic information

species Physcomitrella patens
transcript PP1S91_243V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S91_243V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ14515 (Selaginella moellendorffii), 5'ss of exon 5
TGGGATACCGCTGGTCAGGAGAGGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaataatccggatacgtttgtgcacgtggttgtctgttgcatctaacacctct-ctggatggggctgagtttgattcaattcttaggacttgactg
||||| |||||||| || ||| | |||||||||||||| || || ||||||||||| || ||||| || || || ||   |   |   |   |||| | |||  | | ||   |     || |||| | | || | | | || |                             
TGGGACACCGCTGGGCAAGAGCGCTTCCGGACCATCACCAGCAGTTACTATCGTGGCGCTCACGGGATTATCgtaagc--tggcctata---gtttttccacacgatggtaattc---cctgacacgtttgctcgttcgcgcag-----------------------------
















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|208366025|gb|DC951120.1|DC951120
EST:     CCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: CCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|208377196|gb|DC932346.1|DC932346
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|208372871|gb|DC956272.1|DC956272
EST:     CCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: CCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|100365370|gb|BY966564.1|BY966564
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|208394189|gb|DC933857.1|DC933857
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|100427223|gb|BY959037.1|BY959037
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|208359075|gb|DC957823.1|DC957823
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|162190479|gb|FC365701.1|FC365701
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|162150706|gb|FC327602.1|FC327602
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|100429270|gb|BY978026.1|BY978026
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|208367423|gb|DC951313.1|DC951313
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|100375926|gb|BY968230.1|BY968230
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|18342722|gb|BJ174757.1|BJ174757
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|208376325|gb|DC940995.1|DC940995
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|208370470|gb|DC952173.1|DC952173
EST:     CCACGGAATCATT                         GTTGTTTATGATGTGACAGACCNAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: CCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|208366816|gb|DC940130.1|DC940130
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|100435552|gb|BY960970.1|BY960970
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCCAGAGAGCTTNNCA-CA-CGTGAAGCAAT
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTT--CAACAACGTGAAGCAAT
EST: gi|100405284|gb|BY955448.1|BY955448
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|67508428|gb|BJ941295.1|BJ941295
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|100388728|gb|BY970876.1|BY970876
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|208354508|gb|DC953872.1|DC953872
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|208359364|gb|DC939117.1|DC939117
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|208369746|gb|DC941008.1|DC941008
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|67569192|gb|BJ942016.1|BJ942016
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|67728237|gb|BJ978496.1|BJ978496
EST:     CCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: CCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
EST: gi|18330928|gb|BJ162934.1|BJ162934
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAG
EST: gi|67571758|gb|BJ944582.1|BJ944582
EST:     GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATT                         GTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG
genomic: GGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGG

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: 27 (upstream exon), 35 (downstream exon)
Score: 42

TGGGATACCGCTGGTCAGGAGAGGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaata ... ttgattgcagGTTGTTTATGATGTGACAGACCAAGAGAGCTTCAACAACGTGAAGCAATGGTTGAACGAAATTGATCGATACGCCAGCGAGAACGTAAACAAGCTTCTCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGATACCGCTGGTCAGGAGAGGTTCCGGACCATCACAAGTAGCTACTATCGTGGAGCCCACGGAATCATTgtgagaaataatccggatacgtttgtgcacgtggttgtctgttgcatctaacacctctctggatggggctgagtttgattcaattcttaggacttgactg

- - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG