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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttcttttatattacagttgcttagttgcatgcataatctgatttttatattacttttttgcattttatctgcattttgacgtgttggggtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCATCGGAAATGCTTTTAGACGCGTGGTGATGGAGTCTTTTTTTATCACCGTG

Basic information

species Physcomitrella patens
transcript PP1S337_26V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os03g50885.1 (Oryza sativa), 3'ss of exon 3
gtatttcttttatattacagttgcttagttgca--tgcataatctgatttttatattacttttttgcattttatctgcattttgacgtgttggggtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCATCGGAAATGCTTTTAGACGCGTGGTGATGGAGTCTTTTTTTATCACCGTG--
                  |  |    |  ||||      || | || ||     || |  ||  | || |||   | || | |  | ||  |      |||||||||||||| || ||| | ||||||||||| || |||||||| ||||||||  |||||||||| ||       ||  |   |    |  |    ||    |  
----------------gtaaatatacaaatgcagcaatgtagtgtgtttacctcatgaacttgat-caatttgcttacaatgttgcttgccg------ttgcagATGTGGATTGCCAAGGCTGAGTACGACGAGTCTGGCCCATCCATTGTGCACAGGAAATGCTTCTAATTCTTCGG--ACCCAAGAATGCTAAGCCAAGAGGAG

upper sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G152328_T02 (Zea mays), 3'ss of exon 3
gtatttcttttatattacagttgcttagttgcatgcataatctgatttttatattacttttttgcattttatctgcattttgacgtgttggggtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCATCGGAAATGCTTTTAGACGCGTGGTGATGGAGTCTTTTTTTATCACCGTG
                           ||   |   | || |  ||||     |  | |||   || |  |  |    |      | |    |    |||||||||||||||| ||| | ||||||||||| ||||||||||| || || ||  |||||||||| ||                                   
---------------------------gtaaaacaaacaaacaaatttcgcattcgcatttcctcaatcaaggtctgctcacgattttgcttgcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCACAGGAAATGCTTCTAA----------------------------------

upper sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G152328_T01 (Zea mays), 3'ss of exon 4
gtatttcttttatattacagttgcttagttgcatgcataatctgatttttatattacttttttgcattttatctgcattttgacgtgttggggtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCATCGGAAATGCTTTTAGACGCGTGGTGATGGAGTCTTTTTTTATCACCGTG
                           ||   |   | || |  ||||     |  | |||   || |  |  |    |      | |    |    |||||||||||||||| ||| | ||||||||||| ||||||||||| || || ||  |||||||||| ||      |||    |     |            |  
---------------------------gtaaaacaaacaaacaaatttcgcattcgcatttcctcaatcaaggtctgctcacgattttgcttgcgactgcagATGTGGATCGCCAAGGCCGAGTACGACGAGTCCGGCCCATCCATCGTCCACAGGAAATGCTTCTAATTCTTTGGGCCCGAGAAATGCAAGCCGTGGGGGA

upper sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA13G41060.1 (Glycine max), 3'ss of exon 3
gtatttcttttatattacagttgcttagttgcatgcataatctgatttttatattacttttttgcattttatctgcattttgacgtgttggggtttt----tgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCATCGGAAATGCTTTTAGACGCGTGGTGATGGAGTCTTTTTTTATCACCGTG
     || |  || ||       |    | | |   | ||| |  |||| ||||      |||       || |  ||  ||| |   | |  |||     ||||||||||||| |||||| | |||||||| || ||||| || |||||||| ||  ||||||||||||                                    
-----tcatgcat-ttgtgcactccccctagaaattagaatgttgttttgatatggtcaatttagtagggatattaatgatgaggcacttgtttttggaaatgcagATGTGGATTGCGAAGGCAGAGTACGATGAGTCCGGTCCTTCAATTGTACACAGGAAATGCTTTTGA----------------------------------

upper sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA19G00850.1 (Glycine max), 3'ss of exon 3
gtatttcttttatattacagttgcttagttgcatgcataatctgatttttatattacttttttgcat-tttatctgcattttgacgtgttggggtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCATCGGAAATGCTTTTAGAC-GCGTGGT-GATGGAGTCTTTTTTTATCACCGTG
          | | || | |||  ||| |   |||  |||| | | | ||| | || |  |||| ||  ||        |   |  ||| |   |   ||||||||||||| |||||| | ||||||||||| || || ||||||||||| ||| | || ||||| || |  |  |||| ||| | ||  ||    |  |     
---------gtctgtttctgttctttaat---atgactaat-taactatta-actattgctttgaatgcttgctaatgatacaaactgtcgct-tgagtgcagATGTGGATTGCGAAGGCAGAGTACGACGAGTCTGGACCATCAATTGTTCATAGAAAGTGCTTCTAAATTGTTTGGTTGATAGGGTTATTGAAGAAAAAGA--

upper sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA05G09290.3 (Glycine max), 3'ss of exon 4
gtatttcttttatattacagttgcttagttgcatgcataatctgatttttatattacttttttgcattttatctgcattttgacgtgttggggtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCATCGGAAATGCTTTTAGAC-GCGTG-GTGATGGAGTCTTTTTTTATCACCGTG
          ||| || | |||  ||| |   |||  ||||   | | ||   ||   |  ||||   | ||    ||| |  |   ||| |     ||||||||||||| |||||| | ||||||||||| || || ||||||||||| ||| | || ||||| || |  |  || |  || | ||  ||    |  |     
---------gtatgtttctgttctttaat---atgattaatg-aactattgctttgaatgcttgctaatgatacaaattatcgc---ttgag-----tgcagATGTGGATTGCGAAGGCAGAGTACGACGAGTCTGGACCATCAATTGTTCATAGAAAGTGCTTCTAAATTGTTTGAGCAATAGGGTTATTGAAGAAAAAGA--

upper sequence: PP1S337_26V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: Vv06s0004g04570.t01 (Vitis vinifera), 3'ss of exon 4
gtatttcttttatattacagttgcttagttgcatgcataatctgatttttatattacttttttgcattttatctgcattttgacgtgttggggtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCATCGGAAATGCTTTTAGAC--GCGTGGTGATGGAGTCTTTTTTTATCACCGTG
 ||| |  | | | || |||    ||  || | | ||      ||||| |   | |  |       |  ||   | | |   | ||| |     |  ||||||||||||| || ||| | ||||| || ||||| || ||||| ||||||||| |||||||||| || |   ||  | ||  ||||         | | | || 
ctatattctctgtttttcagacattttttttcct-cactccaagatttgttcttgatgtagcaatttgctacaagtactg-aatgtgatatttgtaatgcagATGTGGATAGCAAAGGCAGAGTATGATGAATCTGGGCCATCTATTGTGCATAGGAAATGCTTCTAAATTGGCCAGATGGGGGAGGTAGAAGAAAGC-CAGT-

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|37849318|gb|BJ607326.1|BJ607326
EST:     GTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAG                         ATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCAT
genomic: GTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAGgtatttcttt ... gtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCAT
EST: gi|37852898|gb|BJ610906.1|BJ610906
EST:     GTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAG                         ATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCAT
genomic: GTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAGgtatttcttt ... gtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCAT
EST: gi|67698456|gb|BJ958689.1|BJ958689
EST:     GTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAG                         ATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCAT
genomic: GTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAGgtatttcttt ... gtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCAT
EST: gi|67727843|gb|BJ978102.1|BJ978102
EST:     GTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAG                         ATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTNCAT
genomic: GTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAGgtatttcttt ... gtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCAT
EST: gi|162177739|gb|FC354573.1|FC354573
EST:     GTGTATGGATCGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAG                         ATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCAT
genomic: GTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAGgtatttcttt ... gtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCAT

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: 29 (upstream exon), 34 (downstream exon)
Score: 6

ACCATCGAGCATGAAGATAAAGGTGGTGGCGCCGCCAGAGAGGAAGTACAGTGTATGGATAGGAGGGTCTATTTTGGCATCTCTCAGTACCTTCCAACAGgtatttcttt ... gtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCATCGGAAATGCTTTTAGACGCGTGGTGATGGAGTCTTTTTTTATCACCGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatattacttttttgcattttatctgcattttgacgtgttggggtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCATCGGAAATGCTTTTAGACGCGTGGTGATGGAGTCTTTTTTTATCACCGTG
                              ttttgac  putative branch site (score: 6)
                                              tttttgc  putative PPT
          ttttttgcattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttcttttatattacagttgcttagttgcatgcataatctgatttttatattacttttttgcattttatctgcattttgacgtgttggggtttttgcagATGTGGATCGCGAAGTCGGAGTACGACGAATCCGGCCCATCAATTGTGCATCGGAAATGCTTTTAGACGCGTGGTGATGGAGTCTTTTTTTATCACCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA