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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaactgaaccattctgctggttacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttttgttttttgcag

Basic information

species Zea mays
transcript GRMZM2G415007_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 3
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaac--tgaaccattc---tgct-ggttacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttttgttttttgcag
|||||||||||| ||||||| ||||| ||||| ||||||||||| ||||||||||| |||||||||||||||||||||||||||||||| ||||| ||||||||||||     |  |||||   ||||  |||| ||| ||  ||  || |||  ||  |   | ||| |||||  |    |||  | ||| |||
AGCCCTGAGGAGGTCAGTGCTATGATCCTTGGAAAGATGAAGGAGACTGCTGAGGCATACCTTGGCAAGAAGATCAACGATGCTGTCGTGACTGTTCCTGgttagtaatgacaagacattcatgtgcttagttaactcaagcggtgattctgtggaa--gccattgctcacttc--tgctctttcatgttttcag

upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G36600.1 (Glycine max), 5'ss of exon 3
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaa----ctgaaccattctgctggttacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttttgttttttgcag-------------------
||||||||||| |||||||||||||||||    ||||||||||| ||||| || || | |||||| ||||| || || |||||||| ||||||||||| ||| | |      ||| | ||         |||  |||  |      |   |     | |    ||||      |||||     ||| |  ||                    
AGCCCTGAGGAAATCAGTGCCATGATTCTGACTAAGATGAAGGAAACTGCGGAAGCATTCCTTGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAGgtaactggaagtctggaacaactcatgacttatttctcctgcaatcttgattgttttcttcctgcttttgcttttatgcca-atttctcacattttcctttcaactgtacag

upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 3
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaa----ctgaaccattctgctggttacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttttgttttttgcag-------------------
||||||||||| |||||||||||||||||    ||||||||||| ||||| || || | |||||| ||||| || || ||||| || ||||||||||| ||| | |      ||| | || |   |   |||  || |   |   ||   |     |      ||||    | |||| ||   | | |  ||                    
AGCCCTGAGGAAATCAGTGCCATGATTCTGACTAAGATGAAGGAAACTGCGGAAGCATTCCTTGGAAAGAAAATTAATGATGCCGTGGTCACTGTCCCAGgtaactggaagtctggaacaattcacgacttatttc-aactgcaatttgattgttttcctcctgcttttgcctttat-ttcaatatctcacattttcctttaaaatgcacag

upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G02940.1 (Glycine max), 5'ss of exon 3
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaa----ctgaaccattctgctggttacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttttg-ttttttgcag-------------------
||||||||||| |||||||||||| ||||   |||||||||||| ||||| || || | ||| || ||||| || || |||||||| ||||||||||| ||| | |      ||||| || | |||   |||  |||     |   | || |    | |  |       || ||| | ||    ||| |  ||                    
AGCCCTGAGGAAATCAGTGCCATGGTTCTGATCAAGATGAAGGAAACTGCGGAAGCATTCCTCGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAGgtaactggaagtctgaaacaatttgcgccttatttctccccttcaatttg-attgttttcctcctgcttttgcttttattccaatttctcacatttttgtttcaaatgcacag

upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G02960.1 (Glycine max), 5'ss of exon 3
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaa----ctgaaccattctgctggttacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttttgttttttgcag
||||||||||| |||||||||||||||||   |||||||||||| ||||| || || | |||||| ||||| || || |||||||| ||||||||||| ||| | |      ||| | || |    ||  |  ||    | | | |||||  || || |      || ||| |   |||   |          
AGCCCTGAGGAAATCAGTGCCATGATTCTGACCAAGATGAAGGAAACTGCGGAAGCATTCCTTGGGAAGAAAATTAATGATGCTGTGGTCACTGTCCCAGgtaactggaagtctggaacaattca-tgactttctgattttgcttttatgccaatatctcacattttcctttcaactgtacag----------

upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G28540.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagta-actgaaccat-tctgctggt----tacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttttgttttttgcag
|| ||||||||||| ||||| ||||||||    ||||||||||| || ||||| || |||||||| ||||| ||||| || ||||| |||||||| || |||||||    ||    || | || |||     || || || ||  ||| || |    || || | | ||| ||   | | |||   |||  | ||
AGTCCTGAGGAGATTAGTGCTATGATTCTGACTAAGATGAAGGAGACAGCTGAAGCCTACCTTGGAAAGAAAATCAAGGACGCTGTTGTCACTGTTCCAGgttagtttgttgttatatatgtggtggagaggtatctttattatctgt-atttggtgat-tgattgttta-tttggtgtttttgactttgcgtag

upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G42020.1 (Arabidopsis thaliana), 5'ss of exon 3
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagt--------aactgaaccattctgctggttacctctagtag--------ttgttatgtaaaaatgtggtggcttacttcctta-tgttttgttttttgcag
|| ||||||||||||||||||||||||||    ||||||||||| || || || || |||||||| ||||| ||||| || ||||| |||||||| || |||||||        || |      ||||| |   ||  |   | ||        || |||| |  |   ||| | | ||  ||  ||  |||||   | |  ||||
AGTCCTGAGGAGATCAGTGCCATGATTCTGACTAAGATGAAGGAGACAGCCGAAGCCTACCTTGGAAAGAAAATCAAGGACGCTGTTGTCACTGTTCCAGgttagtttgttgttaattcgggttttctgttatatatgtagtggagagataaatttcttatctgtattggtgattgattgtttatttggtgtttgactatgcgcag

upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0025g02140.t01 (Vitis vinifera), 5'ss of exon 3
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagta--actgaacca--ttctgctggttacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttttgttttttgcag------------------------------------
|||||||||||||||||||| |||||| |    ||||||||||| || ||||| || | |||||| ||||||||||| ||||||||||| ||||| || ||| ||||  |||   | |  |    |  || |  | | | | |       || |    |  ||   |      |    |||||||  ||                                        
AGCCCTGAGGAGATCAGTGCAATGATTTTGACTAAGATGAAGGAGACAGCTGAAGCATTCCTTGGGAAGAAGATCAAGGATGCTGTCGTTACTGTGCCCGgtgagtatcactcttctagatataacgtgtgaggttttgaactgcccgcttacactcttcttgaaatgtgaattagcattttgttcattaggatgttttactcatattagctttccatgcaacccgcag

upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 3
lower sequence: EDP06859 (Chlamydomonas reinhardtii), 5'ss of exon 2
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagta-actgaaccattctgctggttacctcta-gtagttgttatgtaaaaatgtggtggcttacttccttatgttttgttttttgcag------------------------------------
                          ||||   ||||||||||| ||||||||||| ||||| |||||||   ||||  | ||||| ||||| || || |  || |  |  ||  |     ||  | | | | |  |  ||||  ||||  |   | || |     |    || ||  | ||     |  |                                    
--------------------------TCTTCAGAAGATGAAGGACACTGCTGAGGCCTACCTGGGCAAGACTGTCAAGCACGCTGTGGTCACCGTGCCCGCGTACTTTAACGATGCCCAGCGCCAGgtgcgtatgtggcgttgggatgtgtaggag-ggggcacggcggggttgtggatggtgggagggggtggaggggggccagctggcgttggcacggtactcca

upper sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 3
lower sequence: EDP06660 (Chlamydomonas reinhardtii), 5'ss of exon 3
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagt--aactgaaccattctgctggttacctctagtagttgttatgtaaa-aatgtggtggcttacttccttatgttttgttttttgcag----------------------------------
                          ||||   ||||||||||| ||||||||||| ||||| |||||||   ||||  | ||||| ||||| || || |  || |  |||    ||   |  | |||     |  |  ||||  ||||  |  | | ||         | |    |  ||||  | ||| |                                  
--------------------------TCTTCAGAAGATGAAGGACACTGCTGAGGCCTACCTGGGCAAGACTGTCAAGCACGCTGTGGTCACCGTGCCCGCGTACTTCAACGATGCCCAGCGCCAGgtgcgtgcgtggcgttgggatgtgtatgagggggcacggcgggtacggcggggttgtggtgtgctggaggggggccggctggcgttggcacggtactacg

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|211067397|gb|FL344096.1|FL344096
EST:     TGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTG                         CATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTG
genomic: TGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaact ... ttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTG
EST: gi|67031277|gb|CO460026.1|CO460026
EST:     TGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTG                         CATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTG
genomic: TGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaact ... ttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTG
EST: gi|67043231|gb|CO469486.1|CO469486
EST:     TGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTG                         CATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTG
genomic: TGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaact ... ttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTG
EST: gi|148946714|gb|EC891977.2|EC891977
EST:     TGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTG                         CATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTG
genomic: TGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaact ... ttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTG
EST: gi|148970739|gb|EE021473.2|EE021473
EST:     TGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTG                         CATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTG
genomic: TGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaact ... ttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTG
EST: gi|211430777|gb|FL361062.1|FL361062
EST:     CAACGATGCTGTCGTCACTGTCCCTG                         CATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTG
genomic: CAACGATGCTGTCGTCACTGTCCCTGgttagtaact ... ttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTG

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: 47 (upstream exon), 49 (downstream exon)
Score: 96

AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaact ... ttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaact ... ttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 55

AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaact ... ttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 266

AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaact ... ttttttgcagCATACTTCAATGATGCGCAGAGGCAGGCAACCAAGGATGCTGGTGTCATTGCCGGCCTCAATGTTGCTAGGATCATCAATGAGCCAACTGCTGCTGCTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCCTGAGGAGATCAGTGCCATGATTCTTGGCAAGATGAAGGATACTGCTGAGGCGTACCTTGGCAAGAAGATCAACGATGCTGTCGTCACTGTCCCTGgttagtaactgaaccattctgctggttacctctagtagttgttatgtaaaaatgtggtggcttacttccttatgttttgttttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG