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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtttctacttgctcatgaaacttatgaaaagaaatggtgaaatcggggccaatttaactccatctaatctgcag

Basic information

species Zea mays
transcript GRMZM2G052630_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052630_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g03480.4 (Oryza sativa), 5'ss of exon 8
GTTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtttctactt-----gctcatgaaacttatgaaaagaaatggtgaaatcggggccaatttaac-tccatctaatctgcag
|||||||||||| ||||| |||||||| ||||||||||||||||| |||||||||| |  ||||| ||     | | |  |||    |   |  | ||  || | | |   |  || | || |  || |      |||
GTTCAGTACTGCACAGAAGTTGGACAAGCTTGGCATGAGAGGAAGTGACACgtatgtt--ttctatttaagaggataaccaaaagagttgcattagattttgcattagattcgtatcttacatatatttttgacacag

upper sequence: GRMZM2G052630_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA11G15900.1 (Glycine max), 5'ss of exon 9
GTTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatg-atgtttctacttgctcatgaaacttatgaaaagaaatggtgaaatcggggccaatttaactccatctaatctgcag-------------------
 |||| |||||| ||||||||||| |||||||| ||| ||||||| || ||||||| |||  | |  |   | | |||| || |    | | ||  |  | ||     || |||  |||  | |||    ||                    
ATTCAATACTGCCCAGAAATTGGATAAACTTGGGATGCGAGGAAGTGATACgtatgtatgcatatgttctgtga-gaaatttct----atatataatccattcctaatcactttccctcactttaactgacaaaatgggattctgcgggcag

upper sequence: GRMZM2G052630_T02 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA12G07570.1 (Glycine max), 5'ss of exon 9
GTTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtttctacttgctcatgaaacttatgaaaagaaatggtgaaatcggggccaatttaactccatctaatctgcag-------------------
 |||| |||||| ||||||||||| |||||||| ||| ||||||| || ||||||| | |   |  |   | | |||| || |    |   ||  |  | ||    ||| |||  |||  | |||     |                    
ATTCAATACTGCCCAGAAATTGGATAAACTTGGGATGCGAGGAAGTGATACgtatg-tatgcatgttctgtga-gaaatttct----atttataatccattcctaaccactttccctcactttaactgataaaatggaattctgcgggcag

upper sequence: GRMZM2G052630_T02 (Zea mays), 5'ss of exon 7
lower sequence: AT3G45300.1 (Arabidopsis thaliana), 5'ss of exon 9
GTTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgta--tgatgtttctacttgctcatgaaacttatgaaaag-aaatggtgaaatcggggccaatttaactc---catctaa-tctgcag-----
 ||||||||||||||||||||||||||||| || ||| | |||||||| |||||       ||    |  | | |  | |  | || |||  ||||       ||   | |  |||  |||   |||||   ||| | |     
ATTCAGTACTGCTCAGAAATTGGACAAACTAGGAATGCGGGGAAGCGATACgtaatccccattctctcaagataaaaatatctgtgtaaattaaatccctttttcactgtctctttctctctaacatctgtctctcctgagcag

upper sequence: GRMZM2G052630_T02 (Zea mays), 5'ss of exon 7
lower sequence: Vv06s0004g03140.t01 (Vitis vinifera), 5'ss of exon 9
GTTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgat--gtttctacttgctcatgaaacttatgaaaagaaatggtgaaatcggggccaatttaac----tccat---ctaatctgcag
 |||||||||||||||||||| ||||||||||| ||| ||||||| |||||||| |     || ||||    |  |    ||| |         |  |||||  || |   || | |     | |||   | ||  |||||
ATTCAGTACTGCTCAGAAATTAGACAAACTTGGGATGCGAGGAAGTGACACgtaagcctcattactacagcatgctcccccttttttctctcttttctgaaactggagaggatatgataattttcattaacaaaattgcag

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|67030645|gb|CO459394.1|CO459394
EST:     TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACAC                         ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
EST: gi|31354622|gb|CD438979.1|CD438979
EST:     TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACAC                         ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
EST: gi|76936508|gb|DV174756.1|DV174756
EST:     TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACAC                         ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
EST: gi|78105056|gb|DV523474.1|DV523474
EST:     TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACAC                         ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
EST: gi|149079538|gb|EE168523.2|EE168523
EST:     TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACAC                         ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
EST: gi|31360769|gb|CD445126.1|CD445126
EST:     TTCAGGGCTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACAC                         ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
EST: gi|76936507|gb|DV174755.1|DV174755
EST:     TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACAC                         ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
EST: gi|91057188|gb|EB167606.1|EB167606
EST:     TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACAC                         ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
EST: gi|149073457|gb|EE161762.2|EE161762
EST:     TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACAC                         ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
genomic: TTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
EST: gi|110525230|gb|EE029414.1|EE029414
EST:     AATTGGACAAACTTGGCATGAGAGGAAGCGACAC                         ATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG
genomic: AATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGG

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: 46 (upstream exon), 49 (downstream exon)
Score: 38

GTTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 143

GTTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 88

GTTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

GTTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtt ... taatctgcagATGTGAGCTTGTTTTTGAGAACTGCTTTGTGCCACGCGAGAATGTCCTCGGTGAAGAAGGCAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCAGTACTGCTCAGAAATTGGACAAACTTGGCATGAGAGGAAGCGACACgtatgatgtttctacttgctcatgaaacttatgaaaagaaatggtgaaatcggggccaatttaactccatctaatctgcag

- - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - -  AGAGGA