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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCAGGAGGAGCTTGGGACAACGCTAAGAAATATATTGAAAGCGGTGCTTATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaacatttcgtctgtacaattttttctaaatatttcactgacctggtgatgatatatcattaaagatgttaatttagaagcttatctgtatatctcgtttttcaaacatctaaaatgtccaaactttgtgctgcttgctgcttgtttctgttcaacgcaagagctaatttcaggcatattattaattgcag

Basic information

species Physcomitrella patens
transcript PP1S28_200V6.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S28_200V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 5'ss of exon 14
CCGCAGGAGGAGCTTGGGACAACGCTAAGAAATATATTGAAAGCGGTGCTTATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaacatttcgtctgtacaattttttctaaatatttcactgacctggtgatgatatatcattaaagatgttaatttagaagcttatctgtatatctcgtttttcaaacatctaaaatgtccaaactttgtgctgcttgctgcttgtttctgttcaacgcaagagctaatttcaggcatattattaattgcag
| || || || || ||||| || |||||||| || || || |  || |||  ||| || || || || ||  ||||||| || |||||||||||||||||||||||     | || | | | |  |  |||  ||||      |||   ||| | |  | | ||    |  ||||| |   |     | |    ||| |  |  | ||                                                                                         
CTGCTGGTGGTGCCTGGGATAATGCTAAGAAGTACATCGAGACTGGCGCTCTTGGTGGCAAAGGCAGTGAGTCTCACAAGGCTGCAGTTACTGGTGATACgtaagtgttt-tatcttttatgctctacttttcaaatt-----ctgttttgggggt--tgtttctaggactatgttcacacatttcatcaaaaatatgtagcaatatt-----------------------------------------------------------------------------------------

upper sequence: PP1S28_200V6.1 (Physcomitrella patens), 5'ss of exon 15
lower sequence: AT1G78920.2 (Arabidopsis thaliana), 5'ss of exon 14
CCGCAGGAGGAGCTTGGGACAACGCTAAGAAATATATTGAAAGCGGTGCTTATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaacatttcgtctg-tacaattttttctaaatatttcactgacctggtgatgatatatcattaaagatgttaatttagaagct-tatctgtatatctcgtttttcaaacatctaaaatgtccaaactttgtgctgcttgctgcttgtttctgttcaacgcaagagctaatttcaggcatattattaattgcag
| || ||||| ||||||||||| || |||||||| || || | ||| ||   ||| || || || || || |||||||||||||| || ||||||||||||||||||    ||   |||  | |||   |   | ||  ||  | |  ||||   | ||| | |||||| |    || || |  ||  | ||                                                                                                           
CGGCGGGAGGTGCTTGGGACAATGCAAAGAAATACATAGAGACCGGGGCACTTGGGGGCAAAGGAAGTGAAGCTCACAAAGCAGCTGTGACTGGTGATACgtaagta--ttttcgttctacttcaacactcattcaaagttatatt--cctgaatacgatttctcattagaa---ttcatctgaaaattgtag----------------------------------------------------------------------------------------------------------
















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|37831947|gb|BJ589959.1|BJ589959
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|37838818|gb|BJ596826.1|BJ596826
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|162252044|gb|FC428283.1|FC428283
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|37836235|gb|BJ594243.1|BJ594243
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|37852859|gb|BJ610867.1|BJ610867
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|37852045|gb|BJ610053.1|BJ610053
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|37848728|gb|BJ606736.1|BJ606736
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|37833703|gb|BJ591715.1|BJ591715
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|37838853|gb|BJ596861.1|BJ596861
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|37852556|gb|BJ610564.1|BJ610564
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|162255698|gb|FC432112.1|FC432112
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|162164624|gb|FC341919.1|FC341919
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|37853223|gb|BJ611231.1|BJ611231
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
EST: gi|37844974|gb|BJ602982.1|BJ602982
EST:     TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATAC                         GGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT
genomic: TATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCAT

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), 33 (downstream exon)
Score: 10

CCGCAGGAGGAGCTTGGGACAACGCTAAGAAATATATTGAAAGCGGTGCTTATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaac ... ttaattgcagGGTCGGAGATCCTTTTAAGGATACTGCTGGTCCTTCTCTTCACGTGCTCATTAAGATGCTTGCTACTATCACATTGGTCATGGCACCACTCTTTCTGGAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCAGGAGGAGCTTGGGACAACGCTAAGAAATATATTGAAAGCGGTGCTTATGGAGGGAAGGGTAGCGATGCTCACAAAGCAGCAGTTACTGGTGATACgtaagtaaacatttcgtctgtacaattttttctaaatatttcactgacctggtgatgatatatcattaaagatgttaatttagaagcttatctgtatatctcgtttttcaaacatctaaaatgtccaaactttgtgctgcttgctgcttgtttctgttcaacgcaagagctaatttcaggcatattattaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG