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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgtatgatgaattttggattctttgttttaatttttaacatttttctctgaacgatacaagtcatttgtgcctgattttggaacacatcatctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCATTGTTAGGGCAATGGGAAGAGTCGGCCAAGGATTTACGATTGGCATGTC

Basic information

species Physcomitrella patens
transcript PP1S9_386V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_386V6.3 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os02g01030.3 (Oryza sativa), 3'ss of exon 5
attgtatgatgaattttggattctttgttttaatttttaacatttttc--tctgaacgatacaagtcatttgtgcctgattttggaacacatcatctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCATTGTTAGGGCAATGGGAAGAGTCGGCCAAGGATTTACGATTGGCATGTC
    || | | ||   | ||   |  | ||  ||| ||||   ||     | |  || || | |   |  || || |    |       ||| ||     ||||||||||||||||||||||||| |||||     | ||   |||  | ||  || | ||  ||||||| ||  | ||| | ||| | |     ||||   
--cctagggttaacacttgacagtgcggttatattattaattattaggagtattgactatgccacctaggtgcgctttgcataacctgccattattatgtagATTAACCCAGACTCTGCAAAAGGCTACAAAACTCGTGGAATGGCTTATGCTATGCTTGGAAAATGGGAGGAAGCTGCCCATGATCTTCACACAGCATCGA
















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|162275962|gb|FC452030.1|FC452030
EST:     AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
EST: gi|100399659|gb|BY972829.1|BY972829
EST:     AATGAAGAAGCCCGAATGCTGGAATTAGAGACGCTGATGCTGCTATCAGG                         ATTAACCCAGACTCTGCAAAAG
genomic: AATGAAGAAGCC-GAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAG
EST: gi|22492231|gb|BU052154.1|BU052154
EST:     AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
EST: gi|208347568|gb|DC912827.1|DC912827
EST:     AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAAAG-TTACA-GTGCANANGTGAG-CCAAAGCA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
EST: gi|67717655|gb|BJ967914.1|BJ967914
EST:     AAATGAAGAAGCCGAATGCTGCAATTANAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAA
EST: gi|100416732|gb|BY993060.1|BY993060
EST:     AATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATNCA-G                         ATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGC
genomic: AATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTAT-CAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGC
EST: gi|100446593|gb|CJ970892.1|CJ970892
EST:     AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAAAGGTTACCAGTGCAGAGGT
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGT
EST: gi|162164761|gb|FC340483.1|FC340483
EST:     AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
EST: gi|208373792|gb|DC936577.1|DC936577
EST:     AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCNAAGCA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
EST: gi|208349326|gb|DC910385.1|DC910385
EST:     AAATGAAGAAGCCGAATGCTGCAATTANAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAANG-TTACAAGTGCA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCA
EST: gi|67719577|gb|BJ969836.1|BJ969836
EST:     AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGA
EST: gi|67717904|gb|BJ968163.1|BJ968163
EST:     AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCNAAGCA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
EST: gi|100393447|gb|BY953403.1|BY953403
EST:     AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAAAGGT-ACAAGTGCAGAGGTGAGGGCAAAGCA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
EST: gi|162249194|gb|FC421537.1|FC421537
EST:     AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCNAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
EST: gi|208358732|gb|DC942926.1|DC942926
EST:     AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGANGTGAGNCNAA-GCA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
EST: gi|100401417|gb|BY990992.1|BY990992
EST:     AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
EST: gi|208368260|gb|DC935643.1|DC935643
EST:     AAATGAAGAAGCCGAATGCTGCAATTANAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAANG-TTACAAGTGCANANGTGAGGCCAA-GCA
genomic: AAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
EST: gi|162168430|gb|FC344107.1|FC344107
EST:     AAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG                         ATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA
genomic: AAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCA

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: 32 (upstream exon), 35 (downstream exon)
Score: 13

CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAGgtgacttgag ... catctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCATTGTTAGGGCAATGGGAAGAGTCGGCCAAGGATTTACGATTGGCATGTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctgaacgatacaagtcatttgtgcctgattttggaacacatcatctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCATTGTTAGGGCAATGGGAAGAGTCGGCCAAGGATTTACGATTGGCATGTC
                          gcctgat  putative branch site (score: 13)
                             tgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgtatgatgaattttggattctttgttttaatttttaacatttttctctgaacgatacaagtcatttgtgcctgattttggaacacatcatctaacagATTAACCCAGACTCTGCAAAAGGTTACAAGTGCAGAGGTGAGGCCAAAGCATTGTTAGGGCAATGGGAAGAGTCGGCCAAGGATTTACGATTGGCATGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA