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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgatcgctatctattttaaaaacattttccacctgattatatttctttctaactcagaaaacaaagaataaattccatatgctttgttccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG

Basic information

species Zea mays
transcript GRMZM2G130889_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130889_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 6
----tatgatcgct--atctatt--ttaaaaacattttccacctgattatatttctttctaactcagaaaacaaagaataaattccatatgctttgttccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG
     || || |||  ||  |||  ||| |||    ||  ||||||   |||||  |      |  ||     ||  ||  |     | || ||        ||||||||||||||||||||||| |||||||| ||||||||||||||||| |||||| |||||||||||||||| |||||||| || || || |||
catcaataattgctcaatggattgtttataaatgcatttgacctgaaactattttctctctctttggatggtgaaccatgtacattgtgtgttt--------ctgcagGGTGATAGTATCCTTGCTGATTCTGGCACGGAGCAACTTGAATTTATAGCTTTGTCACAGAGGACTGGTGATCCCAAGTATCAACAAAAG

upper sequence: GRMZM2G130889_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------------tatgatcgcta--tctattttaaaaacattttccacctgattatatttctttctaactcagaaaa-------caaaga----ataaattccatatgctttgttccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG
                                                                           | |  ||  |   | ||  |      |||| |  || |  || |||| |  |   | ||||| |         || |     ||| | ||| | || ||| |    | |  ||||||| |||||| | ||||||||||| || || ||||| |||||||| | ||| || || ||||||||||| || || || |||||||||
gtaaattatagaattctgttaatgcatttcagtcttacttaacagtaggagatttgggatattacttaaatgggttgtagtccttgattttaactacctggcattgtttacat--ttttattacccttagagtcagagatatggctttaatgggtttatataatccttgtgtttt-tattttgttaagGGTGAGAGTATCTTGGCAGATTCTGGCACTGAACAACTGGAATTCATTGTTCTATCCCAAAGGACTGGAGACCCGAAGTATCAGCAGAAG

upper sequence: GRMZM2G130889_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------------------------tatgatcgctatctattttaaaaacatt---ttccacctgattatatttctttctaactcaga-aaacaaagaataaat---tccatatgctttgt---tccatctgc---agGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG
                                                                         |  | |   |  |||||||  || |    |||     | || |||| |  |   | ||||| ||| |  |  | |||   |  |||| | ||||   |  || |     ||||||| |||||| | ||||||||||| || || ||||| |||||||| | ||| || || ||||||||||| | ||| || |||||||||
gtaaattatagaattctgtttatgcattcagtcttactgaacactaggagattttggatattacttcaatgggttgtagtccttgattttaactacctggcattctttacgtttttattacccttagagtcagagaaatatggctttaatgggtttatattccttgtgtttttattttgtcaagGGTGAGAGTATCTTGGCAGATTCTGGCACTGAACAACTGGAATTCATTGTTCTATCCCAAAGGACTGGAGACCTCAAGTATCAGCAGAAG

upper sequence: GRMZM2G130889_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 6
---------tatgatcgctatctattttaaaaacattttccacctgattatatttctttctaactcagaaaacaaagaataaattccatatgctttgttccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG
          | | ||  | | || | |  ||     | ||| |||||  |||||   | |  ||        |    ||        | | |||  |||    |  |||| || ||||| ||||||||||||||||| ||||| |||||||| || || || || |||||||| || || || ||||| ||||| |||
tttcactagcaagctca-tgtttaatgtggaa-tgggtaccatctgatc-tatttacatatgtctttcggtttagttgat------tgtttacttctttcttgttttagGGAGACAGTATTCTTGCAGATTCTGGTACTGAGCAGCTTGAATTTATTGCCCTTTCCCAGAGGACAGGGGACCCAAAATATCAGCAAAAG

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|32929134|gb|CF033946.1|CF033946
EST:     ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAAC                         GGTGATAGTATCCTTGCAGATTCTGGTAC
genomic: ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTAC
EST: gi|67028781|gb|CO457530.1|CO457530
EST:     AGCCCATAATCTCTGCATGGACTAAC                         GGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCT
genomic: AGCCCATAATC-CTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCT
EST: gi|60349712|gb|DN216685.1|DN216685
EST:     ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAAC                         GGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCT
genomic: ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCT
EST: gi|32929269|gb|CF034081.1|CF034081
EST:     ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAAC                         GGTGATAGTATCCTTGCAGATTCTGGT
genomic: ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGT
EST: gi|13178345|gb|BG349603.1|BG349603
EST:     ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAAC                         GGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCT
genomic: ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCT
EST: gi|61119084|gb|DN560045.1|DN560045
EST:     ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAAC                         GGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTT
genomic: ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTT
EST: gi|22543150|gb|BU093588.1|BU093588
EST:     ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAAC                         GGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCT
genomic: ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCT
EST: gi|22935539|gb|BU571814.1|BU571814
EST:     ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAAC                         GGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCT
genomic: ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCT
EST: gi|32928872|gb|CF033684.1|CF033684
EST:     ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAAC                         GGTGATAGTATCCTTGCAGATTCTGGTA
genomic: ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTA
EST: gi|32928842|gb|CF033654.1|CF033654
EST:     TAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAAAC                         G-TGATAGTATCCTTGCAGATTCTGGT
genomic: TAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAA-Cgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGT
EST: gi|60342116|gb|DN209089.1|DN209089
EST:     ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAAC                         GGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCT
genomic: ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCT
EST: gi|32929345|gb|CF034157.1|CF034157
EST:     ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAAC                         GGTGATAGTATCCTTGCAGATTCTGGTAC
genomic: ATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTAC

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 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 118

TACAGATCGACTCTTACCTGCTTGGGATACAACATCTGGCATCCCTTATAATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 121

TACAGATCGACTCTTACCTGCTTGGGATACAACATCTGGCATCCCTTATAATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 187

TACAGATCGACTCTTACCTGCTTGGGATACAACATCTGGCATCCCTTATAATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

TACAGATCGACTCTTACCTGCTTGGGATACAACATCTGGCATCCCTTATAATAGAATAAACCTAGCTCATGGACGAGCCCATAATCCTGGATGGACTAACgtgagttact ... ccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttctaactcagaaaacaaagaataaattccatatgctttgttccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG
   ttctaac  putative branch site (score: 201)
                                      ctttgttcc  putative PPT
              aaaacaaagaataaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatgatcgctatctattttaaaaacattttccacctgattatatttctttctaactcagaaaacaaagaataaattccatatgctttgttccatctgcagGGTGATAGTATCCTTGCAGATTCTGGTACGGAGCAACTTGAATTCATAGCTCTGTCACAGAGGACTGGAGATCCCAAATACCAGCAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - -aaaaaca
- - - - - - - - - - - - - - - -cacctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgctt