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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttataatctatgtctgtag

Basic information

species Zea mays
transcript GRMZM2G044027_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
GAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttat-aatctatgtctgtag
|||||||||| || ||||| |||||||||||||| ||||| || |||||||| ||||||||||||||||||||||||||||||| ||                       |||| |||||  ||| ||| |  ||||||   |   || || |  ||   | | |  | |||||   ||||||| |||||||
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatattt-----------------------ttagttcata--cctttttgtcttgtgatg--tactggattgtagttctccttaataagtattttccaatctatctctgtag

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA12G06980.3 (Glycine max), 5'ss of exon 8
GAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttataatctatgtctgtag------------------
||||  |||| |||||||||||||| |||||||| ||||| ||  ||||||| || ||||| |||||||| || || |||||| | | |||||     |     | || ||    |  | |    |   |    ||   |  | |   ||   | |   |  | |||||||  |  |    |||  | |                    
GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCGgtaattccttatctttt--ctccttggcaacatctcattgttgagggcacaaaca-gtagaagttttgcactgccgttaactaataagcaataactcaatgtgatgcttattttcattttttttctctcag

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA11G15010.1 (Glycine max), 5'ss of exon 8
GAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttcatcttgcacttaaactgtaatattagctcatagccctct---ttattgtgtgataactctaggcttatgatttgtcctcagcaatatttataatctatgtctgtag------------------------
||||  |||| |||||||||||||| |||||||| ||||| ||  ||||||| || ||||| ||||||||||| || |||||| | | |||||    ||   || |  |  | |   | | | |  |   | |  |    |  | |  | | ||   | |  |  | |  ||||   |  | ||   | ||  |                        
GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATCGgtaattccttatctttattttttccttttctccttggcaacatctcattgattgagggcacaaacagtacacgttttgcactgctgttaactaataagcaataactcaatgtgatgcttattttcatatttttctctcag

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 7
GAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttataatctatgtctgtag
| || ||||||||||||||||| || |||||||| || |||||  ||||||| ||||| |||||||| ||||| ||||||||   | ||| ||   || |  || |    | | ||  |  |||| |   |||  | |  |   |    || |  ||| | |     | | ||| |  |   | | |||||
GTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTGgtaa-gttgcatttt---ctcaggctctcgcttcaactt-tctccctgtaatttgcatcaacatattctcattgtcctttattccttaaattgtttttgtttcttctttgtag

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 8
GAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttataatctatgtctgtag
| ||  ||||||| ||||||||||| |||||||| || |||||  ||||||| || ||||| ||||| ||||| || |||||       | |||   ||      |  | |||   |  | |   ||| | ||  |   || | |     | |   ||||        ||||||   |             
GTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAGgtaac------ttttgtgtttt-----tttttttaatcctgaacaaacttcaatgaatatgaagttttaatatgtatgttgtttct--ttatattttggacag----------

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 8
GAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatactt--catcttgcacttaaactgtaatattagctcatagccctctttat---tgtgtgataactctaggcttatgatttgtcct-cagcaatatttataatctatgtctgtag-------------------------------------------------------------------
|||||||||| || ||||||||||| ||||| || || || || |||||||| || ||||||||||||||||| || ||||| | |   |  | |     | | |  ||     | | || || |  |   |    |         | ||  |    ||||  |   |  |  | | || |    ||    ||                                                                       
GAGTCAGGAGTTGCTATGATGAGGGAAAGCGAGTGGCTGAAACTCTGATGTTTGATTATCACAGGCAGCATGGAATAGgtaaaattgggctccctctctctgatccatacacccaacacacagacacccccacacctacacacattcactcagtcactgatgggatgtgtaaaattgttcactcccttcccctccctctctctatctgaaactctactttccaatgcactctcactttattttgaaatggtgatcctataacag

upper sequence: GRMZM2G044027_T02 (Zea mays), 5'ss of exon 8
lower sequence: PP1S189_118V6.1 (Physcomitrella patens), 5'ss of exon 8
GAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgta-atacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttataatctatgtctgtag
|||| || ||||| ||||| ||||| |||||||| || ||||| || ||||| ||||| || |||||||||||| |||||| |||| |   || |   |  | || |  ||  || | | |  |       || | ||      | | |  ||  |   |        |||||||| || ||          
GAGTAAGAAGCTGCTATGACGAGGGAAAGCGTGTTGCTGAGACTCTTATGTTTGACTACCATAGGCAGCATGGCGTTGgtatatacatt-cctcgtgttgtatcttttcta--agttaacacgctctacgcttttatgtcggtccaatgtgtactagaagcgt---aaaatattta-aacctggc-------

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|149097834|gb|EE183762.2|EE183762
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|32841175|gb|CD980856.1|CD980856
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|14206834|gb|BG840512.1|BG840512
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|32909997|gb|CF014809.1|CF014809
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|6194647|gb|AW146751.1|AW146751
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCAAGGAAGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|32841101|gb|CD980782.1|CD980782
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|7216734|gb|AW562856.1|AW562856
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|211032180|gb|FL277400.1|FL277400
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|32850262|gb|CD989943.1|CD989943
EST:     GCGTGTAGCAGAGACGCCGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|32850632|gb|CD990313.1|CD990313
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|32850554|gb|CD990235.1|CD990235
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|213173372|gb|FM186537.1|FM186537
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|488218|gb|T18799.1|T18799
EST:     GACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|32850616|gb|CD990297.1|CD990297
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|148945878|gb|EC891170.2|EC891170
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|32840343|gb|CD980024.1|CD980024
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|32840626|gb|CD980307.1|CD980307
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|32849033|gb|CD988714.1|CD988714
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|67016223|gb|CO444972.1|CO444972
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|67013235|gb|CO441984.1|CO441984
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGGCCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|213192508|gb|FM182601.1|FM182601
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|32165003|gb|CD670321.1|CD670321
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
EST: gi|148951041|gb|EC896695.2|EC896695
EST:     GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG                         AAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG
genomic: GCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttc ... atgtctgtagAAATCCGAATTGCCAGGATTTTCAACACCTATGGACCAAGGATGAACATTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaatacttcatcttgcacttaaactgtaatattagctcatagccctctttattgtgtgataactctaggcttatgatttgtcctcagcaatatttataatctatgtctgtag

- - - - - - - - - - - - - - - - - - - - -  GCTGAT