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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCCCCGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTGGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagttttttttttccatggttggcgattgagcactcgtagtgaacttggggaacaacgctgacttatgcttcgcttgctttcgctggtag

Basic information

species Zea mays
transcript GRMZM2G019986_T04
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019986_T04 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 5'ss of exon 14
ACCCCCGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTGGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagttttttttttcc-----atggttggcgattgagcactcgtagtgaacttggggaa-caacgctgacttatgctt---------cgcttgctttcgctggtag
||||| |||||||| ||||| |||||||| || ||||| || |||||||| || || || |||||||||||||| || || || || ||||| ||||||||||  |||| |  |       |   |  |  | |   ||     |   |||  ||  ||   |   |  ||| | ||           | ||| ||| ||| ||||
ACCCCTGATAGCGCAAAGCTGATGCTGCTTCGTCTCCATAGTAGATGGGTAGTTGCTGCTGGTGGCTTCTTGACCCATTCTGTCCCATTGTACATGACAGgtaaattttctcctgtccaatacattcagaaacttgccaagaacaaaaaacaaggaaaaatgatattttcttttactaatattgtcatgattgattttgcttgtag
















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|149111355|gb|EE294858.2|EE294858
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|78089271|gb|DV517645.1|DV517645
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|16925748|gb|BM078816.1|BM078816
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|211210620|gb|FL436849.1|FL436849
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCTTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|110497708|gb|EE015394.1|EE015394
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|211406613|gb|FL094209.1|FL094209
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|16919474|gb|BM074209.1|BM074209
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|5124174|gb|AI745798.1|AI745798
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|211288805|gb|FL433953.1|FL433953
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|211442520|gb|FL447109.1|FL447109
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|61118750|gb|DN559711.1|DN559711
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|18169117|gb|BM338957.1|BM338957
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|16379775|gb|BI993142.1|BI993142
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|71430550|gb|DR811600.1|DR811600
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|71774723|gb|DR972601.1|DR972601
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|18649167|gb|BM497986.1|BM497986
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|18172348|gb|BM347736.1|BM347736
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|148935255|gb|EC879292.2|EC879292
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|18166601|gb|BM336440.1|BM336440
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|37387607|gb|CF631001.1|CF631001
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|110214878|gb|EC896775.1|EC896775
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTGGAAGTTTCCCCGCTTTCCTCTTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|10450879|gb|BE924803.1|BE924803
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|40335845|gb|CK369915.1|CK369915
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|18164359|gb|BM334198.1|BM334198
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|149102321|gb|EE287688.2|EE287688
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|67018099|gb|CO446848.1|CO446848
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|37375243|gb|CF624047.1|CF624047
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|18166599|gb|BM336438.1|BM336438
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|6022083|gb|AW067011.1|AW067011
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|18167755|gb|BM337595.1|BM337595
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|17931736|gb|BM268696.1|BM268696
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
EST: gi|40303710|gb|CK348097.1|CK348097
EST:     GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAG                         GCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA
genomic: GGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGA

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: 48 (upstream exon), 49 (downstream exon)
Score: 64

ACCCCCGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTGGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGATCTGCCGCGGGCGAACGTTCCATGCACCCAGCGAGATATCGTTTTAGGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 67

ACCCCCGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTGGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGATCTGCCGCGGGCGAACGTTCCATGCACCCAGCGAGATATCGTTTTAGGA


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 49

ACCCCCGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTGGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGATCTGCCGCGGGCGAACGTTCCATGCACCCAGCGAGATATCGTTTTAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 388

ACCCCCGATAGCGCGAAGCTCATGCTGCTCCGCCTCCACAGCAGATGGGTGGTCGCCGCCGGTGGCTTCTTGACGCACTCCGTGCCCTTGTATATGACAGgtagtttttt ... tcgctggtagGCGTCGAAGTTTCCCCGCTTTCCTCCTACGCCGGAGAGAACCTGGAAGCGATCTGCCGCGGGCGAACGTTCCATGCACCCAGCGAGATATCGTTTTAGGA