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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agcggcgtgtcgtggtttggtttatagttctgattacagtcataaattctgtctagtaatcttgtctattctgaaaattaacattggtacttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT

Basic information

species Physcomitrella patens
transcript PP1S12_207V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 3
--------------------agcggcgtgtcgtg-gtttggtttatagt-tctgattacagtcataaattc------tgtctagtaatcttgtctattctgaaaattaaca------ttggtacttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT
                    |  ||   ||| |   | || |  ||  | | ||  || ||| | | |||         ||   | |  | || |||  |||  ||| |        ||  |   || ||  || |||||||||||||| ||||| ||  | || |||||||| || |||||||||||||| |||||| ||||||| ||||||||  | |||||||| || |||
gtagagtagtgcatacttcaaatgggaagtcttctatatgatgaatgttgtttgtgtatagtaaaagattggtggaacttcccatgaaatagtttata-tgagtattgatgaacttttttttttctccttatagGTATGATGCTCATTCGGGTGGAGAGCGTGAAATTCAGAGAACCATGTTGGAGTTGCTTAATCAGCTGGATGGTTTTGATTCAAGGGGAGATGTTAAAGTT

upper sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 3
agcggcgtgtcgtggtttggtttatagttctg----attacagtcataaattctgtctagtaatcttgtctattctgaaaattaacattggt-acttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT
   ||  | ||       || | | | || |     |  |  ||     |  || |||||| |     | || | |||   ||    ||  |  |    ||| || |||||||||||||| ||||| ||  | ||||||||||| || |||||||||||| | |||||| ||||||| ||||||||  | |||||||| || |||
---ggtctttcccttcccggctgagatttttatgaaaaaaatgttgctgaagct-tctagtgaaaggat-taatatgagttttgctgtttctcgccctgttgtagGTATGATGCTCATTCTGGTGGTGAGCGTGAGATTCAGAGAACCATGTTGGAGTTGTTAAATCAGCTGGATGGTTTTGATTCAAGAGGAGATGTTAAAGTT

upper sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA03G32800.1 (Glycine max), 3'ss of exon 3
----------------------------------------------agcggcgtgtcgtggtttggtttatagttctgattacagtcataaatt----------ctgtctagtaatcttgt----ctattctgaaaattaacattggtacttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT
                                                |    |    |  | || ||| |  ||| |      | ||     |           | |  ||| || |  |    | ||||| |  ||     |   |  | |||||||| |||||||| || || ||||| ||| | || ||||||||||||||||||||||||||||| ||||| ||||| ||||||||  | ||||| || || |||
gtaagttattgaacatcagctttaggagtcactgtgtcaagacattttctatcttcttttttctgatttttttttccgggagggggcaggggatgcgggactggttatagagtgatatcatggatcaattcttagtatatgtctcttttatgcattgcagGTATGATGCCCACTCTGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGACGTAAAAGTT

upper sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA10G04920.1 (Glycine max), 3'ss of exon 3
----------------------------agcggcgtgtcgtggtttggtttatagt-tctgattacagtc-ataaattctgtctagtaatcttgtctattctgaaaattaacattgg-tacttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT
                            |     ||  || || | |     |  |  ||  |  || || || |  |||    | |  | |  |  ||||   |  ||| || |   ||  |  || ||| ||||||||||| |||||||| ||| | |||||||| ||||| ||||| ||||||||||| ||||| ||||| ||||||||| | |||||||| || || 
gtaattttaacccccaactttagctgtcatgaaggtaccggggatggaagagtgatgccttgtatcactctatgagctcttgggattcttttcctacattcatgagcttaccagtaaatatgtatttacagGTATGATGCTCACTCAGGTGGAGAACGTGAGATTCAAAGGACCATGTTAGAGTTGCTGAACCAGTTAGATGGTTTTGATTCTAGAGGAGATGTAAAAGTG

upper sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------------agcggcgtgtcgtggtttggtttatagttctgattacagtcataaattctgtctagtaatctt-gtctattctgaaaat-taacattggtacttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT
                                                                   |  || |  || |||||      |    |  |||||   |       |  |  ||   |  ||| ||||| |  || |  |  |  || | | |||||| |||||||| || |||||||| ||| | || ||||||||||||||||||||||||||||| ||||| ||||| || |||||  | || ||||| || || 
gtaagttatcgagtatcagcttctggagtcactgttttaagacattttctatcctctttttccggatgtagttttttgttttgggaggaggcagggggtacaggactggtagaagagtgatatcatgagtcaattcttattatatgtctcttata-tgctttgcagGTATGATGCCCACTCAGGTGGAGAACGTGAAATTCAGAGGACTATGTTGGAGTTGCTGAACCAGTTAGATGGTTTCGATTCAAGAGGTGATGTTAAAGTG

upper sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA11G27200.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------agcggcgtgtcgtggtttggtttatagttctgattacagtcataaattctgtcta---gtaatctt----gtctattctgaaaat-taacattggtacttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT
                                                             | |  ||| ||  ||| ||||   |    || ||  |  | ||     ||  |   || || |     ||| ||||| |  || |  |  |  || | | |||||| |||||||| || ||| |||| ||| | || ||||||||||||||| ||||||||||||| ||||| ||||| || |||||  | || ||||| || || 
gtaagttatcaagtatcagcttctagagtcactgttttaagacattttctatcctctttttccggatgtagtttttttgttttgggag--gagtaggggtacaagactagtagaagagtgatatcatgagtcaattcttattatatgtctcttata-tgctttgcagGTATGATGCCCACTCAAGTGGAGAACGTGAAATTCAGAGGACTATGATGGAGTTGCTGAACCAGTTAGATGGTTTCGATTCAAGAGGTGATGTTAAAGTG

upper sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA13G19280.1 (Glycine max), 3'ss of exon 3
------------------------------agcggcgtgtcgtggtttggtttatagt-tctgattacagtc-ataaattctgtctagtaatcttgtctattctgaaaattaaca-ttggtacttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT
                                 ||   |  | |||| |     |  | |||  |  || || || |  |||    | |  | |  |  ||||   |  |||  | |   ||  |  || ||| ||||||||||| ||||| || ||| | || ||||| ||||| ||| | ||||||||||| ||||| ||||| ||||||||  | ||||||||||| || 
gtaattttaacctccaactttagtattcatgaaggtagggtggggttggaagagtgatgtcttgtatcactctatgagctcttaggattcttttcctacattcatgagcttactaataaatatgtatttacagGTATGATGCTCACTCAGGAGGAGAACGTGAAATTCAAAGGACCATGCTAGAGTTGCTGAACCAGTTAGATGGTTTTGATTCAAGAGGAGATGTGAAAGTG

upper sequence: PP1S12_207V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 3
agcggcgtgtcgtggtttggtttatagttctgattacagtcataaattctgtctagtaatcttgtctattctgaaaattaacattggtacttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT
           |||  | | |  | | |  |||| | |      |||  | | |   ||  |  | | || |   ||||| ||    || | | |||||| ||||||||||| |||||||| ||| | || || |||||||| ||||||||  |||| || ||||| || || ||||||||  | |||||||| || || 
-----------gtgagtcgatgaacattagtgatgaaa------aatcatatttttcaagttcttttttttttttaattatca--aatattcc-ttgcagGTATGATGCTCACTCAGGTGGTGAACGTGAAATCCAGAGGACCATGTTGGAACTGCTAAACCAGTTAGACGGTTTTGATTCAAGGGGAGATGTCAAAGTG

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|37827368|gb|BJ585380.1|BJ585380
EST:     TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAG                         ATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
genomic: TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAGgtacttttcg ... ttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
EST: gi|162179027|gb|FC356428.1|FC356428
EST:     TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAG                         ATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
genomic: TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAGgtacttttcg ... ttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
EST: gi|162233611|gb|FC409370.1|FC409370
EST:     TTGACGAAATTGATGCAGTGGGTACAAAGAG                         ATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
genomic: TTGACGAAATTGATGCAGTGGGTACAAAGAGgtacttttcg ... ttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
EST: gi|208350798|gb|DC925929.1|DC925929
EST:     TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAG                         ATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
genomic: TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAGgtacttttcg ... ttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
EST: gi|162179026|gb|FC356427.1|FC356427
EST:     TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAG                         ATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
genomic: TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAGgtacttttcg ... ttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
EST: gi|208374231|gb|DC945277.1|DC945277
EST:     TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAG                         ATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
genomic: TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAGgtacttttcg ... ttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
EST: gi|208372234|gb|DC948037.1|DC948037
EST:     TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAG                         ATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
genomic: TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAGgtacttttcg ... ttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
EST: gi|208370715|gb|DC948252.1|DC948252
EST:     TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAG                         ATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
genomic: TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAGgtacttttcg ... ttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
EST: gi|67723618|gb|BJ973877.1|BJ973877
EST:     TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAG                         ATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
genomic: TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAGgtacttttcg ... ttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
EST: gi|208379248|gb|DC927259.1|DC927259
EST:     TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAG                         ATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
genomic: TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAGgtacttttcg ... ttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
EST: gi|162278370|gb|FC454248.1|FC454248
EST:     TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAG                         ATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA
genomic: TCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAGgtacttttcg ... ttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGA

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: 31 (upstream exon), 32 (downstream exon)
Score: 5

GGGATGGACCTAAGTTGGTGCGAGAGTTATTTCGGGTCGCGGATGAATTATCTCCTTCCATTGTCTTTATTGACGAAATTGATGCAGTGGGTACAAAGAGgtacttttcg ... ttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctgtctagtaatcttgtctattctgaaaattaacattggtacttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT
                              aattaac  putative branch site (score: 5)
                                            cttcatt  putative PPT
                     tattctgaaaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agcggcgtgtcgtggtttggtttatagttctgattacagtcataaattctgtctagtaatcttgtctattctgaaaattaacattggtacttcattgcagATATGATGCTCATTCAGGTGGGGAAAGAGAGATTCAGAGGACTATGTTGGAGTTGCTGAATCAGTTGGATGGATTTGATTCTCGTGGAGATGTGAAGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG