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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcctacattttatctgaagaatagggaaataatgcgactatattcctacattgaccggtactttgtgtaacatggagcatctcattcccatttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTAC

Basic information

species Zea mays
transcript GRMZM2G124919_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147714_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g29180.1 (Oryza sativa), 3'ss of exon 4
ctgcctacattttatctgaagaatagggaaataatgcga---ctatattcctacattgaccggtactttgtgtaacatggagcatctcattcccatttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTAC
  |  | |  || |    || | ||    ||| ||||       ||||| |||  |||| |  || ||  | || |||| |  | |||||||    ||||||||||||||||||||||| |||||||| || |||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||| ||||||||||||||
--gtgtcctattgaaaaaaaaattataagaatgatgccgtattaatatttctatcttgatcaatatttcctttagcatgaaa-acctcattcttccttctcagGATATGGTGGTGATGTCTGGTTCCCCCAACCAGCACCAAAGGATCACCCATGGCGATACATGCCTAATCATGCCATGACCCCTCATATCTCTGGGACTAC

upper sequence: GRMZM2G147714_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
ctgcctacattttatctgaagaatagggaaataatgcgactatattcctacattgaccggtactttgtgtaacatggagcatctcattccc--atttct-cagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTAC
 | ||||  || | |    |   |  |    |  | | | |   ||  ||  ||| |   ||||   | |  |||      ||  | || |  ||||||  ||| ||| |||||||||| ||||||||||||||||| ||||||||||| || ||||| |||||||| |||||||||||||| ||||| || ||||| || ||
-tccctaagttctgttatgatcctttgttgttgttactattcc-tttttaagttg-caattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC

upper sequence: GRMZM2G147714_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 4
--ctgcctacatttt-atctgaagaatagggaaataatgcgactatattcctacattgaccggtactttgtgtaacatggagcatctcattcccatttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTAC
   ||   | |||   |||| |    |   ||  |        | ||   |  |||||     |  ||| | |  | |     || || |    | |    ||| |||||||||||||| |||  |  ||| ||||| |||||||| || || |||||||||||||| |||||||||||||| ||||| || ||||| || ||
gtttgttcatattcccatctaagttgttcagaggtggcaaagttttacatcatcattgctaattgttttcttttcctttccaaatttctt---aaatctatagGCTATGGTGGTGATGTTTGGCCCATACAACCAGCTCCAAAGGACCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC

upper sequence: GRMZM2G147714_T01 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA19G01210.4 (Glycine max), 3'ss of exon 4
--ctgcctacattttatctgaagaatagggaaataatgcgactatattcctacattg--accggtactttgtgtaacatggagcatctcattcccatttct-cagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTAC
  |||     ||  | | |      | ||    |  | | | |   ||  ||  |||  |  | || ||| | | |               ||  ||||||  ||| ||| |||||||||| ||||||||||| ||||| ||||||||||| || |||||||||||||| |||||||||||||| ||||| || ||||| || ||
ttctgttatgatccttttttt----ttggttgttgttactattcc-tttttaagttgcaattgctaatttttttcatcctctttccaaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAACCAGCTCCAAAGGATCATCCATGGCGCTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGTACCAC

upper sequence: GRMZM2G147714_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 3'ss of exon 4
-----ctgcctacatttt---atctgaagaatagggaaataatgcgactatattcctacattgaccggtactttgtgtaacatggagcatctca--ttcccatttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTAC
      |  |  || |||    | |   | ||  |   ||  ||   | || || ||   ||   | ||  |    |  |       ||| | |  || |   || ||||| ||  |||| ||||| ||||  ||||||||||| || ||||| || || ||||| |||||||| ||||| || ||||||||||| || ||||| || ||
gtaatgtttcagcacttttgagtttcttggatttgagtatgttgtt-caatgtttct-ttttatgcagttttgaaagccaatgacttcattttaattttctgattttcagGTTACAGTGGGGATGTTTGGTATCCACAGCCAGCCCCCAAGGACCATCCATGGCGGTACATGCCAAACCAAGCTATGACCCCTCATATTTCTGGCACCAC

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|31354982|gb|CD439339.1|CD439339
EST:     CATGGATGCTCAAGCAGTCGCAGATGCATGTTCTAGCGGTCACATTGCTG                         GATACGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCT
genomic: CATGGATGCTCGAGCAGTCGCAGATGCATGTTCTAGCGGTCACATTGCTGgtacttacta ... catttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCT
EST: gi|32849118|gb|CD988799.1|CD988799
EST:     CATGGATGCTCAAGCAGTCGCAGATGCATGTTCTAGCGGTCACATTGCTG                         GATACGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCT
genomic: CATGGATGCTCGAGCAGTCGCAGATGCATGTTCTAGCGGTCACATTGCTGgtacttacta ... catttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCT
EST: gi|32916182|gb|CF020994.1|CF020994
EST:     CATGGATGCTCAAGCAGTCGCAGATGCATGTTCTAGCGGTCACATTGCTG                         GATACGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCT
genomic: CATGGATGCTCGAGCAGTCGCAGATGCATGTTCTAGCGGTCACATTGCTGgtacttacta ... catttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCT
EST: gi|32863793|gb|CF003475.1|CF003475
EST:     CATGGATGCTCAAGCAGTCGCAGATGCATGTTCTAGCGGTCACATTGCTG                         GATACGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCT
genomic: CATGGATGCTCGAGCAGTCGCAGATGCATGTTCTAGCGGTCACATTGCTGgtacttacta ... catttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctacattgaccggtactttgtgtaacatggagcatctcattcccatttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTAC
                     gtgtaac  putative branch site (score: 3)
                                    tctcattcccatttct  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcctacattttatctgaagaatagggaaataatgcgactatattcctacattgaccggtactttgtgtaacatggagcatctcattcccatttctcagGATATGGTGGTGATGTGTGGTTCCCACAGCCAGCACCAAAGGATCACCCCTGGCGCTACATGCCTAACCATGCCATGACCCCTCACATCTCTGGGACTAC

- gcctaca
- -cctacat
- - - - - - - - -gaagaata
- - - - - - - - - - - - - ggaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgga