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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCTAACAACACATTGGAAAGGGTTGCTCCCCTGACTCATGCCGTGGGGAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgtggacaaagtggttgtgtttgtggagtgagggggaggttgggacatgcagcagagttgtgtaggatgatgcggggacgggtggcggcgtgttggaatgttgatggaggagttgggtatggagaatggaatagagtggagtgatgttgtgagaaggtttgtaacggcgggattggtggtttgcag

Basic information

species Physcomitrella patens
transcript PP1S450_22V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G070605_T01 (Zea mays), 5'ss of exon 10
CTTGCTAACAACACATTGGAAAGGGTTGCTCCCCTGACTCATGCCGTGGGGAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgtggacaaagtggttgtgtttgtggagtgagggggaggttgggacatgcagcag-agttgtgtaggatgatgcggggacgggtggcggcgtgttggaatgttgatggaggagttgggtatggagaatggaatagagtggagtgatgttgtgagaaggtttgtaacggcgggattggtggtttgcag
 ||||||  ||||| |||||  | || ||||| ||||| ||||| ||||| || ||||||||||| |||||||| || || ||||| ||||| || || |||||||    |                   | |  |      |  | || ||  |   ||   || |   ||  |   |||     |     |                                                                                                     
ATTGCTACGAACACCTTGGAGCGAGTGGCTCCTCTGACACATGCTGTGGGCAATGTGTTGAAGCGTGTGTTTGTCATTGGCTTCTCAATCGTTGTTTTTGgtgagtggacgacagtccccccccccccccttgttttcccctgctgctgtgatgtaatgctctagctagctaacact-tgctaaacctcacag-----------------------------------------------------------------------------------------------------

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: AT5G46110.3 (Arabidopsis thaliana), 5'ss of exon 10
CTTGCTAACAACACATTGGAAAGGGTTGCTCCCCTGACTCATGCCGTGGGGAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtg--agtttgtggacaaagtggttgtgtttgtggagtgagggggaggttgggacatgcagcagagttgtgtaggatgatgcggggacgggtggcggcgtgttggaatgttgatggaggagttgggtatggagaatggaatagagtggagtgatgttgtgagaaggtttgtaacggcgggattggtggtttgcag
|| |||| ||| || ||||| |||||||| || |||||||| || || || |||||  |||| || ||||| |||||||| |||||||||||  | ||||||   || ||    ||    |  |  | | | |  | | |   |     |     ||| |||| | |    ||   | |   |   |    | || |                                                                                                  
CTGGCTACCAATACCTTGGAGAGGGTTGCACCGCTGACTCACGCGGTTGGAAACGTTCTGAAACGTGTGTTCGTGATCGGTTTCTCCATCGTTATCTTCGgtacaagattactaacctc-tcttcatatatttttacttattagaccaatcccgaatgaagca-attcaaatacttttacttgtcaaatatttgcag--------------------------------------------------------------------------------------------------

upper sequence: PP1S450_22V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv01s0011g00600.t01 (Vitis vinifera), 5'ss of exon 10
CTTGCTAACAACACATTGGAAAGGGTTGCTCCCCTGACTCATGCCGTGGGGAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtg--agtttgtgg------acaaagtggttgtgtttgtggagtgagggggaggttgggacatgcagcagagttgtgtaggatgatgcggggacgggtggcgg--cgtgttggaatgttgatggaggagttgggtatggagaatggaatagagtggagtgatgttgtgagaaggtttgtaacggcgggattggtggtttgcag
||||||| |||||| |||||| ||||||| || || || ||||| || || || |||||||||||||| ||||| || || |||||||| ||  | ||||||    |||  |         |||| || || |||      |   |     |  ||   | || ||| | |  |    |    ||| |           ||    |    || | |     | |     |||  |    |     | | |   |||                                               
CTTGCTACCAACACCTTGGAACGGGTTGCGCCGCTTACACATGCAGTTGGAAATGTGTTGAAGCGAGTTTTTGTCATTGGATTCTCCATTGTTATATTCGgtattggttcattcctcccctcaaaatgatt-tgtgccgccaactaactctaaatttccatat-cagaaaaacttcagacctcgattcaatatttatcagccatcctcactgaactaactcttgttttcttgtattctaatggctgcaaaatctggcag--------------------------------------------

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|162227036|gb|FC402561.1|FC402561
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|67701339|gb|BJ961572.1|BJ961572
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|162227035|gb|FC402560.1|FC402560
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|67727399|gb|BJ977658.1|BJ977658
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|37845320|gb|BJ603328.1|BJ603328
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|67726423|gb|BJ976682.1|BJ976682
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|67726208|gb|BJ976467.1|BJ976467
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|67725255|gb|BJ975514.1|BJ975514
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|208374047|gb|DC948916.1|DC948916
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|208363899|gb|DC946956.1|DC946956
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|208367830|gb|DC954903.1|DC954903
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|67723662|gb|BJ973921.1|BJ973921
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|37836875|gb|BJ594883.1|BJ594883
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|208357256|gb|DC949900.1|DC949900
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|37826879|gb|BJ584891.1|BJ584891
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|208385509|gb|DC956679.1|DC956679
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
EST: gi|67725418|gb|BJ975677.1|BJ975677
EST:     GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCG                         GCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG
genomic: GAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAG

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), 32 (downstream exon)
Score: 29

CTTGCTAACAACACATTGGAAAGGGTTGCTCCCCTGACTCATGCCGTGGGGAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgt ... tggtttgcagGCAACAAGATCTCGACCCAGACTGGGATCGGAACAGCCATTGCTATTGGAGGAGTGGCGTTGTACTCTTTTATCAAGGCAAGACAGGAGGAAGCGAAGAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCTAACAACACATTGGAAAGGGTTGCTCCCCTGACTCATGCCGTGGGGAACGTGTTGAAGCGAGTGTTTGTGATCGGGTTCTCCATCGTGGTGTTCGgtgagtttgtggacaaagtggttgtgtttgtggagtgagggggaggttgggacatgcagcagagttgtgtaggatgatgcggggacgggtggcggcgtgttggaatgttgatggaggagttgggtatggagaatggaatagagtggagtgatgttgtgagaaggtttgtaacggcgggattggtggtttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC