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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCCATCATTGTTTGATGTGTTGGTGATGCCTAATCTTTATGGTGATATCATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttagcctctcaaagcttacatcgaccttcgatcacattcctcagctgtgaggattggttttcaccacaacaaaagtagtagctaggatttaagc...

Basic information

species Physcomitrella patens
transcript PP1S199_33V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S199_33V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: LOC_Os01g16900.3 (Oryza sativa), 5'ss of exon 7
ACCCATCATTGTTTGATGTGTTGGTGATGCCTAATCTTTATGGTGATATCATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttagcctctcaaagcttacatcgacctt-cgatcacattcctcagctgtgag-gattggttttcaccacaacaaaagtagtagctaggatttaagc
| ||     | ||||||||  |||||||||| ||||||||||||||||| || || ||| | |||||||| || ||||| || || || ||||| || |||||| |||    | |      ||  ||| |  |  |   ||  |    || |    |   | |  ||| |||     ||                       
ATCCTGGTCTTTTTGATGTACTGGTGATGCCAAATCTTTATGGTGATATTATTAGTGATCTTTGTGCTGGTCTGATTGGAGGCTTGGGCTTGACACCCAGgtaaatttg--ttattgtttgttctatcaatttgacatccaggtaatacaacgccaactaactattttgcactctcccag----------------------

upper sequence: PP1S199_33V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT3G09810.1 (Arabidopsis thaliana), 5'ss of exon 5
ACCCATCATTGTTTGATGTGTTGGTGATGCCTAATCTTTATGGTGATATCATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttagcctctcaaagcttacatcgaccttcgatcacattcctcagctgtgaggattggttttcaccacaacaaaagtagtagctaggatttaagc
||||| || | |||||||| ||||||||||| ||||| ||||| ||||| ||||||||||| |||||||||||| |||| ||  ||||| |||| |||||||||  || |  |||      |  ||  ||   | |   |   |    |  || |   ||    ||   |    |  |   |     | ||         
ACCCAGCACTTTTTGATGTCTTGGTGATGCCAAATCTCTATGGAGATATTATCAGCGATTTGTGTGCTGGACTTGTTGGGGGACTAGGACTGACTCCTAGgtaacatttgtttcttcg---tctcacagattattgtctag--tatgaaaatgaggcaatcatcttatgctcttattatgttttgttccag---------

upper sequence: PP1S199_33V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: Vv08s0040g01700.t01 (Vitis vinifera), 5'ss of exon 5
ACCCATCATTGTTTGATGTGTTGGTGATGCCTAATCTTTATGGTGATATCATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaa----gtttagcctctcaaagcttacatcgaccttcgatcacattcctcagctgtgaggattggttttcaccacaacaaaagtagtagctaggatttaagc
| ||  |  | ||||||||||||||||||||||| || |||||||| || || || ||| | ||||||||  | ||||| ||  |||| || || || |||||      ||||  || |||    | |  |  |   |  ||     ||||||  | |     | || || |  ||||                          
ATCCTGCGCTTTTTGATGTGTTGGTGATGCCTAACCTCTATGGTGACATTATTAGTGATCTCTGTGCTGGCTTGATTGGGGGACTAGGCTTAACACCAAGgtatcttcatttattctatcatctttaatttatatgattcatatagatcctcacatctt----tcggcttcctacacag-------------------------

upper sequence: PP1S199_33V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ18109 (Selaginella moellendorffii), 5'ss of exon 6
ACCCATCATTGTTTGATGTGTTGGTGATGCCTAATCTTTATGGTGATATCATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttagcctctcaaagcttacatcgaccttcgatcacattcctcagctgtgag-gattggttttcaccacaacaaaagtagtagctaggatttaagc
| ||  | |||||||| |||||||||||||| ||  | ||||| ||||||||||| ||| | || ||||| || || |||||  | |||||||| || ||||||||     ||||| |   ||   |||       |||||  | ||| | |||||  ||   |                                     
ATCCTGCCTTGTTTGACGTGTTGGTGATGCCAAACTTGTATGGAGATATCATCAGTGATCTCTGCGCTGGTCTCATAGGCGGCCTTGGATTGACACCGAGgtaagta----ctctcga---ttgggtcgcgaaagaatcac--tgctctg-tgtgaccgaccag-------------------------------------

upper sequence: PP1S199_33V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ09610 (Selaginella moellendorffii), 5'ss of exon 5
ACCCATCATTGTTTGATGTGTTGGTGATGCCTAATCTTTATGGTGATATCATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttagcctctcaaagcttacatcgaccttcgatcacattcctcagctgtgag-gattggttttcaccacaacaaaagtagtagctaggatttaagc
| ||  | |||||||| |||||||||||||| ||  | ||||| ||||||||||| ||| | || ||||| || || |||||  | |||||||| || |||||||||    ||||| |   ||   |||       |||||  | ||| | |||||  ||   |                                     
ATCCTGCCTTGTTTGACGTGTTGGTGATGCCAAACTTGTATGGAGATATCATCAGTGATCTCTGCGCTGGTCTCATAGGCGGCCTTGGATTGACACCGAGgtaagtt----ctctcga---ttgggtcgcgaaagaatcac--tgctctg-tgtgaccgaccag-------------------------------------

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|162171537|gb|FC347839.1|FC347839
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|18340057|gb|BJ172085.1|BJ172085
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|67726238|gb|BJ976497.1|BJ976497
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|162246372|gb|FC419934.1|FC419934
EST:     GTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: GTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|162174845|gb|FC351637.1|FC351637
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|37853210|gb|BJ611218.1|BJ611218
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCNTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|162235877|gb|FC411620.1|FC411620
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|67725138|gb|BJ975397.1|BJ975397
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|67696691|gb|BJ956924.1|BJ956924
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|162261041|gb|FC437435.1|FC437435
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|208375010|gb|DC956406.1|DC956406
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|162182686|gb|FC359433.1|FC359433
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|208361101|gb|DC957552.1|DC957552
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|37836533|gb|BJ594541.1|BJ594541
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|18336310|gb|BJ168332.1|BJ168332
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|162155666|gb|FC331279.1|FC331279
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|162261042|gb|FC437436.1|FC437436
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|37826181|gb|BJ584193.1|BJ584193
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|67724281|gb|BJ974540.1|BJ974540
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|37844324|gb|BJ602332.1|BJ602332
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|162174844|gb|FC351636.1|FC351636
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|208385227|gb|DC923593.1|DC923593
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
EST: gi|208367531|gb|DC954963.1|DC954963
EST:     ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAG                         TGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC
genomic: ATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAAC

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: 18

ACCCATCATTGTTTGATGTGTTGGTGATGCCTAATCTTTATGGTGATATCATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttag ... tgggtaatagTGGAAATATTGGAGACAATGGATTGGCCTTGATGGAAGCCGTTCACGGAACAGCTCCTGATATCGCTGGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCCATCATTGTTTGATGTGTTGGTGATGCCTAATCTTTATGGTGATATCATCAGCGATTTATGTGCTGGACTTATTGGCGGTTTAGGATTGACCCCTAGgtaagtttagcctctcaaagcttacatcgaccttcgatcacattcctcagctgtgaggattggttttcaccacaacaaaagtagtagctaggatttaagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caacaaaa