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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgcctctccctgtttgcaatatgtttggtgttgcctgtcactcgagaaattaagtcaagactgcaccataatttattctgttcatatatctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAG

Basic information

species Zea mays
transcript GRMZM2G129513_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G129513_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os08g44810.1 (Oryza sativa), 3'ss of exon 9
gtatgtgcctctccctgtttgcaatatgtttggtgttgcctgtcactcgagaaattaagtcaagactgcaccataatttattc----tgttcatatatctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAG
                        || |   || || |  || |   |   || |||   |   | ||     || ||| |||      ||| ||| | | ||||||||||||| || ||||| ||||||||||||||||| ||||||||||| ||||| ||||| || |||||||||||||| ||||| |||| |||||||||||
-----------------------gtaagcccggagt-gtatgccctacatcaatttataactgaattgatgtttactttgttcgcttcattcctatgtttcaacagCGTGGAGGAGTACTCATACAAAAATGGGGCAGATCTTCAGCTGCATCAACCGCCGTTTCCATCGTGGATGCTATTAGGTCCCTTGTAAATCCTACCCCAG

upper sequence: GRMZM2G129513_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G34150.3 (Glycine max), 3'ss of exon 9
gtatgtgcctctccctgtttgcaatatgtttggtgttgcctgtcactcgagaaattaagtcaagactgcaccataatttattctgttcatatatc-taaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAG
    ||     |    ||| ||  |   |       | | ||       ||| ||  |||      ||  | | ||  |     ||   | | |  |   ||| | || ||||  || || ||||||||||| ||||||||||||||||| ||  |||| || || || ||||| || |||||  | ||||||||||| || |
----gtaaaatttgtagttagcg-tccatagctaaatacatgatgtaaaagatatgtagtttcc-ttgtgctaaaagctgacaagtaattgtttgattggcagAGAGGTGGTGCACTTATTCAAAAATGGGGAAGATCATCAGCTGCATCAACTTCTGTGTCAATTGTTGATGCCATAAGATCTTTAGTAACTCCTACTCCCG

upper sequence: GRMZM2G129513_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G34150.2 (Glycine max), 3'ss of exon 9
gtatgtgcctctccctgtttgcaatatgtttggtgttgcctgtcactcgagaaattaagtcaagactgcaccataatttattctgttcatatatc-taaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAG
    ||     |    ||| ||  |   |       | | ||       ||| ||  |||      ||  | | ||  |     ||   | | |  |   ||| | || ||||  || || ||||||||||| ||||||||||||||||| ||  |||| || || || ||||| || |||||  |                 
----gtaaaatttgtagttagcg-tccatagctaaatacatgatgtaaaagatatgtagtttcc-ttgtgctaaaagctgacaagtaattgtttgattggcagAGAGGTGGTGCACTTATTCAAAAATGGGGAAGATCATCAGCTGCATCAACTTCTGTGTCAATTGTTGATGCCATAAGATCTTTA----------------

upper sequence: GRMZM2G129513_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA20G33380.1 (Glycine max), 3'ss of exon 11
-----gtatgtgcctctccctgtttgcaatatgtttggtgttgcctgtcactcgagaaattaagtcaagactgcaccataatttattctgttcatatatctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAG
      | |||   |  |     | || | ||   ||||||     |  | |  ||       ||   ||  ||   | || | |||  |||  | |   |   ||| | || |||| ||| || ||||||||||| ||||||||||||||||| ||  |||| || || || ||||| || |||||  | ||||||||||| || |
gtaaattttgtaattagcatacatagctaaatacatggtgtaaaaagata-tgtagtttccttgtgctgaaagc-tgacaagtaatt--gtttgtttgattgg-cagAGAGGTGGTGCGCTTATTCAAAAATGGGGAAGATCATCAGCTGCATCAACTTCTGTGTCAATTGTTGATGCCATAAGATCTTTAGTAACTCCTACTCCCG

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|15554238|gb|BI644236.1|BI644236
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|110219294|gb|EC901192.1|EC901192
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGTTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|78089786|gb|DV518160.1|DV518160
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|32916975|gb|CF021787.1|CF021787
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTACTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|211195515|gb|FL441324.1|FL441324
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|13198702|gb|BG354504.1|BG354504
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|32825533|gb|CD965255.1|CD965255
EST:     TAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|148971653|gb|EE022376.2|EE022376
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGTTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|211178869|gb|FL449312.1|FL449312
EST:     AGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCC-AAAATGGGGGCAGATCATCAGCTGCATCGAC
genomic: AGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAAT-GGGGCAGATCATCAGCTGCATCGAC
EST: gi|15590379|gb|BI674995.1|BI674995
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|148928691|gb|EC873304.2|EC873304
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|211129427|gb|FL299354.1|FL299354
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|211195516|gb|FL441325.1|FL441325
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|32791146|gb|CD943382.1|CD943382
EST:     TAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGAGC
genomic: TAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|30706123|gb|CD059034.1|CD059034
EST:     TTAAGGATACCCAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|74239371|gb|DT647285.1|DT647285
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|13558383|gb|BG549739.1|BG549739
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|13490961|gb|BG517725.1|BG517725
EST:     TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
genomic: TTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC
EST: gi|12968102|gb|BG265049.1|BG265049
EST:     GGAAGAGTTCACCCTCACAGTTCAAAAG                         CGTGGAGGTGTGCTCATCCAAAAATGGGGCAGTTCATCAGCTGCATCGACC
genomic: GGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACC

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: 49 (upstream exon), 45 (downstream exon)
Score: 48

TCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 855

TCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAG


Block sizes: 37 (upstream exon), 47 (downstream exon)
Score: 6

TCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 611

TCCTGATTTCTTGAATGCCAAAATTGATGGAAGACCAGTGAAAGAAGTCATTAAGGATACCAAGTGGTTAGAGGAAGAGTTCACCCTCACAGTTCAAAAGgtatgtgcct ... atctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagaaattaagtcaagactgcaccataatttattctgttcatatatctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAG
                         ataatttattctgttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgcctctccctgtttgcaatatgtttggtgttgcctgtcactcgagaaattaagtcaagactgcaccataatttattctgttcatatatctaaacagCGTGGAGGTGTGCTCATCCAAAAATGGGGCAGATCATCAGCTGCATCGACCGCTGTTTCGATAGTGGATGCTATTAGATCCCTCGTAACTCCTACCCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA