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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggtgtcgtgatcaacagaatcaggttaaatccacatttcaacaaccatgagatgttttccaccgacttaagtggttccttattttaatttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG

Basic information

species Physcomitrella patens
transcript PP1S29_256V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S29_256V6.2 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 10
----tttggtgtcgtgat-caacagaatcaggttaaat-----ccacatttcaacaaccatgagatgttttccaccgacttaagtggttccttattttaatttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG
    |||  |  ||| || |    |||  |     |||     |   || |         |||| | ||   |   | ||| |    |  | ||      |    |  ||| ||  |    ||| |||| |||||||| ||||| ||||||||  | |||||  | ||||| | || ||||||||||||||| |||||||||   || |
gtacttttatcacgtaatactgttgaagtaaaaggaatattagcagtatattttttttggtgagctattcctctatgccttgacaattaacctacacctgtac-ctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTG
















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|37845830|gb|BJ603838.1|BJ603838
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|162169757|gb|FC345294.1|FC345294
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|37845305|gb|BJ603313.1|BJ603313
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|18327390|gb|BJ159392.1|BJ159392
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCA
EST: gi|162182768|gb|FC359515.1|FC359515
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|162176593|gb|FC353062.1|FC353062
EST:     TTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: TTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|67720249|gb|BJ970508.1|BJ970508
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|67727192|gb|BJ977451.1|BJ977451
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|162176348|gb|FC353533.1|FC353533
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|18334218|gb|BJ166234.1|BJ166234
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|67726751|gb|BJ977010.1|BJ977010
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|162171617|gb|FC347558.1|FC347558
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|162181163|gb|FC357608.1|FC357608
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|162170699|gb|FC346286.1|FC346286
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|37824766|gb|BJ582832.1|BJ582832
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|18335658|gb|BJ167678.1|BJ167678
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|67727852|gb|BJ978111.1|BJ978111
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|162223700|gb|FC399772.1|FC399772
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|19789330|gb|BQ041244.1|BQ041244
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGAT
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGAT
EST: gi|162176594|gb|FC353063.1|FC353063
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|162223699|gb|FC399771.1|FC399771
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|162182767|gb|FC359514.1|FC359514
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|162167231|gb|FC342796.1|FC342796
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|18333553|gb|BJ165568.1|BJ165568
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|67725967|gb|BJ976226.1|BJ976226
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|67720690|gb|BJ970949.1|BJ970949
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|208375034|gb|DC944815.1|DC944815
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|67720235|gb|BJ970494.1|BJ970494
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG                         GTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGA
EST: gi|162241271|gb|FC416902.1|FC416902
EST:     ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGGTAACACCATTTCAGCAG                         GTCCCCTTGAAA-GCAGAGCGGCTAAAGCTATTGG
genomic: ATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCC-TTGAAAAGCAGAGCGGCTAAGGCTATTGG

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), 28 (downstream exon)
Score: 11

GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAGgtaaccaact ... tttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccatgagatgttttccaccgacttaagtggttccttattttaatttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG
                                       ttttaat  putative branch site (score: 11)
                                ttccttattttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggtgtcgtgatcaacagaatcaggttaaatccacatttcaacaaccatgagatgttttccaccgacttaagtggttccttattttaatttattgcagGTCCCTTGAAAAGCAGAGCGGCTAAGGCTATTGGTTTTATTGATGACATGATCAACTACTCCTCTGCTAATGCACCATTGCAAAAGGAGCTGGAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG