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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttaattgcttgcaacctgctagctactgttttttttgccatgtgaccatgtccttgggtttgacttatcttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG

Basic information

species Zea mays
transcript GRMZM2G064023_T03
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 13
-ctttaattgcttgcaacct--gctagctactgttttttttgccatgtgaccatgtccttgggtttgacttatcttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG
  | || ||  ||   || |  | | || | ||  | | |   ||||    ||| ||   |   |   ||  || ||   |  | ||  | || ||  | |||||||||||||||||||||||||||||||||||||| ||||| || || ||||| |||||||| ||| | || ||||| || ||||||
gatatactttttttttacttttgttggccattgcctatctc-tcatg-actcatctctgggcactaacctcttcatcccatacttgtgat-attcaattacagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCATTGCACGGCCTGGCTAATCAG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 13
----ctttaattgcttgcaacctgctagcta-ctgttttttttgccatgtgaccatgtccttgggtttgacttatcttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG
     ||   ||||| ||||    ||  ||  || | | | |    |     | |||  |   |   |   | ||    |||||||| || |||   |||    ||||||||||||||||||||| |||||||||||||| ||||| || || ||||| |||||||| ||  | || ||||| || ||||||
ttattttcttttgctggcaattgcctctctctctctctctctcatgactcatctatgggcactgacctc-ttcattccgtgctcatgatattcaattaca----gGTTGGAAGTGCTCTGTCAGACCCTTATCTTTCTTTTGCAGCTGCACTGAATGGTTTAGCTGGACCGTTGCACGGCCTGGCTAATCAG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 13
------------------------------------------------------------------------ctttaattgcttgcaacctgctagctactgttttttttgc-catgtgaccatgtccttgggtttg-------acttatcttctgct-catggtact---catccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG
                                                                         ||||||   |       |    ||   ||||||| ||    || |    || |   |   | |        |  ||| |  |  |  || |||||     | | | | |||||||  ||| | || ||||||||||||||| | || ||||| ||| | ||||||||||||||||| || |||||  | || ||||||
gtaagttacttcctttaatcaagccctttccattctgtcataatttagaattgtaaaacattaaaaaggattttttaatatatattgtggtaaaggcctgtgtttttattatatatatatatatatatatatatatatatatatatatatatattaatgtattgtactgtgtgttcccgt-cagGTTGCTAGTCCGCTATCAGATCCTTATCTTGCATTTGCAGCTGCTTTGAATGGGTTAGCTGGGCCCCTGCATGGTTTGGCCAATCAG

upper sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 13
ctttaattgcttgcaacctgctagctac-tgttttttttgccatgtgaccatgtccttgggtttgacttat-cttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG
        |  || |   | ||  | |  |||   ||||      |   | |  |    | ||  | |  | ||| |||| |   | ||  | ||  || ||||||| ||||| || ||||| || ||||| || || ||||| ||  ||||||| |||||||||||||| |||||  | || ||||||
--------gtatgta-tatactctccatgtgtcaattttaaaggattgacctacctgaagtttctaatggttcttttgctaaaaattcttgttca--tgtagGTTGGTAGTGCACTTTCAGACCCATATCTGTCATTTGCAGCTGCATTAAATGGTTTAGCTGGGCCACTCCATGGTTTGGCTAATCAG

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|6020672|gb|AW065480.1|AW065480
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttt ... ccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|31361054|gb|CD445411.1|CD445411
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttt ... ccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|6952534|gb|AW424602.1|AW424602
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttt ... ccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT
EST: gi|5915419|gb|AW053060.1|AW053060
EST:     TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTG                         GTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTTGCAGCGGCTCTAAAT
genomic: TGATCATGAAGGCGGGAATGTCAGTGCTCATACTGGTCATCTGgtaatatttt ... ccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccatgtccttgggtttgacttatcttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG
              gtttgac  putative branch site (score: 4)
                                        ctcatcc  putative PPT
                     ttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttaattgcttgcaacctgctagctactgttttttttgccatgtgaccatgtccttgggtttgacttatcttctgctcatggtactcatccacatgcagGTTGGAAGTGCTCTGTCAGATCCTTATCTTTCTTTCGCAGCGGCTCTAAATGGGTTAGCTGGGCCACTACATGGCCTTGCAAATCAG

- - - -tgcttgc
- - - - - - - - cctgcta
- - - - - - - - - - - -gctactg
- - - - - - - - - - - - - - - - - - - gccatgt
- - - - - - - - - - - - - - - - - - - - - - - - catgtcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtact