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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttttatgcacatataagtataaagtagttaccacattgtacaactatttcttacacttttttttgctagaatttgtgtaagtaatgattctcagactttaatatttgaattaaagtatttgtgcttgattaatggtag

Basic information

species Zea mays
transcript GRMZM2G164562_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 5'ss of exon 5
GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttttatgcacatataa-gtataaagtagttaccacattgtacaactatttcttacactt-----ttttttgctagaatttgtgtaagtaatgattctcagactt-taatatttgaat---taa--agtatttgtgcttgatt-aatggtag
||||||||||||||| ||||||| |||||||| || |||||||||||||| ||||||||||| || || |||||||| |||||||||| ||||||       ||||| || |||  |||  |   ||||| || |  |  | |   || |     | | ||  | |||| | |  || |  || | |  | |||| |  || ||||||   |||  |  || |    |  |   |||| |||
GATTACAGTGAAATGGCTAAGGCCTACAGACCTTCACATGCAGATGCAACTTATGACTTCAAATACGGTGTTAGAGCAGTGCAGgtactttttttcatgttttataatgtgtaatatagccatt-cattgaaccatcaactgtagtacctaaacttctcttatttgaatgtctaaaactg-tggtacctaaacttctcttacttgaatgcctaaccaacatcttctatcaaccgaatgatag

upper sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 5
lower sequence: AT1G48850.2 (Arabidopsis thaliana), 5'ss of exon 5
GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttttatgcacatataagtataaagtagttaccacattgtacaactatttcttacacttttttttgctagaatttgtgtaagtaatgattctcagactttaatatttgaattaaagtatttgtgcttgattaatggtag
|||||||||||||||||    || || |||||||| ||||| |||||||| |||||| | |||||||| || ||| | ||||||||| ||||||        | | |  || |   |  | | || ||        |  | |||    | | ||     | |||  |     |||     || |  | ||| | |||   | ||                         
GATTACAGTGAAATGTCGGTTGCCTATAGACCATCGCATGCTGATGCAACTTATGACATGAAGTATGGTGTCAGATCAGTGCAGgtatctttttc-------tgttaa-attactcacatgctacttttcttggtaaggtttta----tgtgttcaaaggcattgttcagcttaacataccttaagcgttattcttt---tcaag------------------------

upper sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv06s0004g02960.t01 (Vitis vinifera), 5'ss of exon 5
GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtacctt--ttttatgcacatataagtataaagtagttaccacattgtacaactatttcttacacttttttttgctagaatttgtgtaagtaatgattctcagactttaatatttgaattaaagtatttgtgcttgattaatggtag
||||| || ||  |||| | ||| ||||| || || |||||||||||||||||||| ||||||||||| || |||||  | ||||||      || |  | | ||  |  | |     | |  |||  || |   |    |  ||| |  ||| |   || | |    ||||                                                           
GATTATAGCGAGCTGTCAAGGGCTTACAGGCCTTCTCATGCAGATGCAACCTATGATTTCAAGTATGGTGTAAGAGCAATCCAGgtaaaagggttcttagaaaattcacatttgcctaaatctccatcttcttggatgtatgattata--tttgtcaactggga---atgtag----------------------------------------------------------

upper sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 5
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 5
GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtacctt-ttttatgcacatataagtataaagtagttaccacattgtacaactatttcttacacttttttttgctagaatttgtgtaagtaatgattctcagactttaatatttgaattaaagtatttgtgcttgattaatggtag
||||| |  |||||||| || ||||| || || || ||||||||||| || ||||||||||||||||| || ||  | |||||||||   | ||||  || || ||    || |  |  |    || | | | ||       | | | |||   ||  |  | |||||     | ||| ||       |  |  ||||| || ||| | |                    
GATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAGgtaatgtattttgggctcacattgtaatgacattatgggaac-tggaaaaaaacaaaatgagaatttgacttcatgtagtttgta-gttttatggtt-----gttccacaatttggatgaaaatgtag------------------

upper sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ25489 (Selaginella moellendorffii), 5'ss of exon 5
GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttttatgcacatataagtataaagtagttaccacattgtacaactatttcttacacttttttttgctagaatttgtgtaagtaatgattctcagactttaatatttgaattaaagtatttgtgcttgattaatggtag
||||||   || ||| ||   || ||  | ||||| ||||||||||| || || ||||||||||||||| || ||||||| ||||       || || || |  |   | |  |  |  |  |    |||  | ||      || | | |||||                                                                           
GATTACTCAGAGATGGCTCTAGCTTATCGGCCATCTCATGCAGATGCTACTTACGACTTCAAGTATGGAATTCGAGCTGTCCAGg-------ttaatccaaacttttctttgcaacatctctcggggtgttaagct------taaagtctttttcag------------------------------------------------------------------------

upper sequence: GRMZM2G164562_T01 (Zea mays), 5'ss of exon 5
lower sequence: EFJ22409 (Selaginella moellendorffii), 5'ss of exon 4
GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttttatgcacatataagtataaagtagttaccacattgtacaactatttcttacacttttttttgctagaatttgtgtaagtaatgattctcagactttaatatttgaattaaagtatttgtgcttgattaatggtag
||||||   || ||| ||   || ||  | ||||| ||||||||||| || || ||||||||||||||| || ||||||| |||||      |  || || |  |     |  |  |     |    |||  | ||     | | |  |||||  |                                                                         
GATTACTCAGAGATGGCTCTAGCTTATCGGCCATCTCATGCAGATGCTACTTACGACTTCAAGTATGGAATTCGAGCTGTCCAGgt------taaatccaaacttttccttgcaacatccctcggggtgttaagct-----taaaatctttttcag-------------------------------------------------------------------------

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|149088514|gb|EE177624.2|EE177624
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
EST: gi|28361588|gb|CB239944.1|CB239944
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
EST: gi|149070137|gb|EE158538.2|EE158538
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
EST: gi|211165641|gb|FL126860.1|FL126860
EST:     CCCATGCAGATGCAACCTATGACTTCAAATATGGAGTTAAAGCTGTGCAG                         GGAGGTGGGAAGG-CATCAGCC
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGG-AAGGTCATCAGCC
EST: gi|76020355|gb|DT947525.1|DT947525
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATCAGCCAGAGAAATCATTGGCAGGGTGGCTGCAGGA
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
EST: gi|211165637|gb|FL126856.1|FL126856
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATCAGCCAGAGAA
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAA
EST: gi|149015775|gb|EE045474.2|EE045474
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
EST: gi|71442663|gb|DR823713.1|DR823713
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
EST: gi|148963945|gb|EE015067.2|EE015067
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
EST: gi|28390366|gb|CB250180.1|CB250180
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
EST: gi|60352524|gb|DN219497.1|DN219497
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
EST: gi|78089034|gb|DV517427.1|DV517427
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
EST: gi|149100015|gb|EE186068.2|EE186068
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATC
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATC
EST: gi|148966882|gb|EE018003.2|EE018003
EST:     CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG                         GGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA
genomic: CCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGA

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), 49 (downstream exon)
Score: 221

GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 548

GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 552

GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 572

GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttt ... ttaatggtagGGAGGTGGAAGGTCATCAGCCAGAGAAACCATTGGCAGGGTGGCTGCAGGAGCTCTTGCAAAGAAAATTCTAAAGCTCAAATCAGGAGTGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAGgtaccttttttatgcacatataagtataaagtagttaccacattgtacaactatttcttacacttttttttgctagaatttgtgtaagtaatgattctcagactttaatatttgaattaaagtatttgtgcttgattaatggtag

- - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT