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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCAAAGAGTCAGACACTGGATTGGCAGTGCCCAGTCAGTGGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaactctaaccttgggtgctggcatccggctcggcaaagcagtgcgtattgttgcagagttgctcactggtaaagactcacttgtagtttagttaacttagtttgtttattatggcag

Basic information

species Physcomitrella patens
transcript PP1S49_256V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_256V6.1 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 3
GAATCAAAGAGTCAGACACTGGATTGGCAGTGCCCAGTCAGTGGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaa----ctctaaccttgggtgctggcatccggctcg---gcaaagcagtgcgtattg---ttgcagagttgctcactggtaaagactcacttgtagtttagttaactta-gtttgtttatta-tggcag------------------
| || || ||||| || || || |||||    || || |||||||||||||| || || ||||| ||||||||||| ||||||||  | || |||| | ||    | || |  ||| ||     | |     |       | |||  || ||  ||   |  ||    || |   ||||| | |     |||   |  | || || |  | | ||  |||| |  |                    
GTATAAAGGAGTCTGATACAGGGTTGGCTCCACCTAGCCAGTGGGATTTGGTTTCAGATAAACAGATGATGCAAGAAGAACAACCGTTACAAgtatattaaatgaccctgatattgtgttacttcgtagattttacttttacagctttgagttatgacctaccatgcatgatagttggtagaaatctttttggtttcaattttacatgtgctagtgcattaataacttctctttctctttctgcag
















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|67717642|gb|BJ967901.1|BJ967901
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|208348229|gb|DC905485.1|DC905485
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|100393232|gb|BY989787.1|BY989787
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|67507498|gb|BJ940380.1|BJ940380
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|100442037|gb|BY962930.1|BY962930
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|100451078|gb|CJ974586.1|CJ974586
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|208384192|gb|DC911300.1|DC911300
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|100435405|gb|BY979227.1|BY979227
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|208375716|gb|DC936656.1|DC936656
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|100445251|gb|BY982880.1|BY982880
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|67716993|gb|BJ967252.1|BJ967252
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|100441014|gb|BY962502.1|BY962502
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|100385842|gb|BY951036.1|BY951036
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|208397607|gb|DC912225.1|DC912225
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|208387130|gb|DC941302.1|DC941302
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|100355304|gb|BY965094.1|BY965094
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|67704545|gb|BJ964778.1|BJ964778
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|100352668|gb|BY945387.1|BY945387
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|18361561|gb|BJ193627.1|BJ193627
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|67719122|gb|BJ969381.1|BJ969381
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|100417415|gb|BY957319.1|BY957319
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|100352747|gb|BY945428.1|BY945428
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTAC
EST: gi|67576591|gb|BJ949415.1|BJ949415
EST:     GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAG                         GTTGCTAGGTGTACAAAA
genomic: GGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAA

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: 25 (upstream exon), 31 (downstream exon)
Score: 11

GAATCAAAGAGTCAGACACTGGATTGGCAGTGCCCAGTCAGTGGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaac ... attatggcagGTTGCTAGGTGTACAAAAATTATCAATGCCAATACGGATGACTCCAAGTACGTCATCAATGTGAAGCAGATTGCTAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATCAAAGAGTCAGACACTGGATTGGCAGTGCCCAGTCAGTGGGATTTGGTATCGGACAAACAAATGATGCAAGAGGAACAACCACTGCAGgtatgtaaactctaaccttgggtgctggcatccggctcggcaaagcagtgcgtattgttgcagagttgctcactggtaaagactcacttgtagtttagttaacttagtttgtttattatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG