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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatatcttgctaatatgttacaagagtaatattttgttagtgcctcctctactgttccacctgaaggaaaaaataacactgatatgctgatttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA

Basic information

species Zea mays
transcript GRMZM2G043056_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g11820.1 (Oryza sativa), 3'ss of exon 2
----acatatcttgctaatatgt-tacaagagtaatattttgttagtgcctcctctactgttccacctgaaggaaaaaataacactgatatgctgatttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA
    || ||  | |    ||| | |  || | | || |    ||| |   |   ||| | ||     |  |  |   ||| |||    |||  |||| | |||||||||||||||||||||| |||||||||||||||||  |||||||||||||||||||| ||||
gtagacttaattagtgggtatttgtgtaatactgatgtgc-attactttgtttcctaattttttttgtatattactgaatcaca----tatattgatattaacagGGACCACAATATGTCTGTACAAATTTCTGGACCTTCATTTGTACCAATTGCAGTGGAGCACA

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G35310.1 (Glycine max), 3'ss of exon 2
-acatatcttgctaatatgttacaagagtaatattttgttag-tgcctcctctactgttccacctgaaggaaaaaataacactgatatgctgatttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA
     ||  | || | |  |  | ||   | | |||  || | ||       |   |       ||  | |  ||||     |    | ||   |||   |||||||||||||||| ||||||||||||||||| |||||||| || || || || |||  |||
attgcattcttctga-acctagctaggaaattttttaatttgatgttgaggtttgagactagtttgttgcattaaatccttttttctttctctcttgt-tagGGACCACAATATGTGTGCACAAATTTCTGGACGTTTGTTTGCACTAACTGTAGCGGAATACA

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G04420.2 (Glycine max), 3'ss of exon 1
-acatatcttgctaatatgttacaagagtaatattttgttag-tgcctcctctactgttccacctgaaggaaaaaataacactgatatgctgatttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA
     ||  | || | || |  | ||   | | ||   || | ||       |   |       ||  | |  ||||     |    | ||   |||   |||||||||||||||| ||| ||||||||||||| |||||||| |  || || || |||  |||
attgcattcttctga-atctagctaggaaattgttgaatttgatgttgatatttgagactagtttgctgcattaaatccttttttctttctctcttgt-tagGGACCACAATATGTTTGCTCAAATTTCTGGACGTTTGTTTGCATTAACTGTAGCGGAATACA

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G09750.2 (Glycine max), 3'ss of exon 2
acatatcttgctaatatgttacaagagtaatattttg--ttagtgcctcctctactgtt-ccacctgaaggaaaaaataacactgatatgctgatttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA
    || ||| |    |  | ||  |   | | |     ||| ||| |    || |||  |           |  ||| |  ||  | | ||  |||||| |||||||||||||||| |||||||| |||||||| |||||||| || || |||||||||  |||
-agcattttgattgcgttcttcagaacctagaatggaaattattgcatttgatattgtgactggtcttttatattaattat-cttcttttctcttttgaa-agGGACCACAATATGTGTGCACAAACTTCTGGACGTTTGTTTGCACAAACTGCAGTGGAATACA

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G13350.2 (Arabidopsis thaliana), 3'ss of exon 2
acatatcttgctaatatgttacaagagtaatattttgttagtgcctcctctactgttcc---acctgaaggaaaaaataacactgatatgctgatttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA
           |||  | ||    |      ||||  | | | ||      | | ||     | || || |  ||  |  |          | ||||    |||||||||||||||| ||||| | ||||||||| |||||||||||||| |||||||||  |||
----------gtaagtttttttttgctcttcatttgatcatttccgataaaaattttgagagaacttaacgttaacgtttcttcttcgatatcatttacttagGGACCACAATATGTTTGCACTACTTTCTGGACTTTTGTTTGTACCAACTGCAGTGGAATACA

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv11s0016g04210.t01 (Vitis vinifera), 3'ss of exon 1
acatatcttgctaatatgttacaagagtaatattttgttagtgcctcctctactgttccacctgaaggaaaaaat-aacactgatatgctgattt-gaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA
|  | | | |   | |     ||  |   | ||| | | | |  ||     |   |   |  |     |  | || ||  || || |  |  ||   |||||||||| ||||| || ||||||||||||||||| |||||||| || | ||| |||||   |||
aattttgtagtccaaagagctcaccaactacattct-tcattaacttggaaag-atgaaatatagtctatgatatgaaggctaattttttccttccaaacagGGACCGCAATACGTGTGCACAAATTTCTGGACATTTGTTTGCACAACTTGTAGTGGGATACA

upper sequence: GRMZM2G043056_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv09s0002g04860.t01 (Vitis vinifera), 3'ss of exon 2
acatatcttgctaatatgttacaagagtaatattttgttagtgcctcctctactgttccacctgaaggaaaaaataacactgatatgctgattt-gaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA
|  | | ||| | | |  ||||    ||  | |||  ||           |||  |       || | | |  || |     || | ||| ||| || |||||||||||||| |||||||||||||||||||| |||||||| || |  |||||||||  |||
aattttgttgtttaaagtttacttttgtgctctttgatttagaatgaaaataccatgttgtgagatg-ataccatgaattaaatcttctgtttttgagcagGGACCACAATACGTCTGCACAAATTTCTGGACATTTGTTTGCACAACCTGCAGTGGAATACA

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|78087088|gb|DV515481.1|DV515481
EST:     GCCTGCTGAAGCTGCCCGCCAACAAGCGCTGCATCAACTGCAATAATTTG                         GGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGC
genomic: GCCTGCTGAAGCTGCCCGCCAACAAGCGCTGCATCAACTGCAATAATTTGgtgagtatgt ... atttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGC
EST: gi|211246821|gb|FL131900.1|FL131900
EST:     GCCTGCTGAAGCTGCCCGCCAACAAGCGCTGCATCAACTGCAATAATTTG                         GGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGC
genomic: GCCTGCTGAAGCTGCCCGCCAACAAGCGCTGCATCAACTGCAATAATTTGgtgagtatgt ... atttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGC
EST: gi|71428282|gb|DR809332.1|DR809332
EST:     GCCTGCTGAAGCTGCCCGCCAACAAGCGCTGCATCAACTGCAATAATTTG                         GGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGC
genomic: GCCTGCTGAAGCTGCCCGCCAACAAGCGCTGCATCAACTGCAATAATTTGgtgagtatgt ... atttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGC
EST: gi|211246819|gb|FL131898.1|FL131898
EST:     GCCTGCTGAAGCTGCCCGCCAACAAGCGCTGCATCAACTGCAATAATTTG                         GGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGC
genomic: GCCTGCTGAAGCTGCCCGCCAACAAGCGCTGCATCAACTGCAATAATTTGgtgagtatgt ... atttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGC
EST: gi|78115033|gb|DV533421.1|DV533421
EST:     GCCTGCTGAAGCTGCCCGCCAACAAGCGCTGCATCAACTGCAATAATTTG                         GGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGC
genomic: GCCTGCTGAAGCTGCCCGCCAACAAGCGCTGCATCAACTGCAATAATTTGgtgagtatgt ... atttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctctactgttccacctgaaggaaaaaataacactgatatgctgatttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA
                       aaaaaataaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatatcttgctaatatgttacaagagtaatattttgttagtgcctcctctactgttccacctgaaggaaaaaataacactgatatgctgatttgaacagGGACCACAATATGTCTGCACAAATTTCTGGACCTTTGTTTGTACCAATTGCAGTGGATCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - -ttgctaa
- - - - - - - - - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgctg