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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaacggattcacttttcttcgattctcattgagtatttcccttccatctattgtgtattcttcacaaattttttggtgtgtcttgcag

Basic information

species Zea mays
transcript GRMZM2G069198_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G069198_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g46310.1 (Oryza sativa), 5'ss of exon 3
AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaacggattcacttttcttcgattctcattgagtatttcccttccatctattgtgtattcttcacaaattttttggtgtgtcttgcag
||||| |||||||||||| |||| |||||||||||||| |||||||| ||||| ||||| ||||||||||||||||| ||||||||    |||||   | |||     |  | | ||||||||  |         | ||   ||     | | | | | |      ||||||||
AAAAATAGTTGGAAGAACCTATTTTCATACATAGGGCCCGGATTTCTTGTCTCTATTGCGTATATTGATCCTGGAAATTgtaagatagctggatttgttgttcactcctattaaatgagtattcac---------agtgatcatgaccaaaagaatctct----catcttgcag

upper sequence: GRMZM2G069198_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G00590.1 (Glycine max), 5'ss of exon 2
AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaacggattcac--ttttcttcgattctcattgagtatttcccttccatctattgtgtattcttcacaaattttttggtgtgtcttgcag
|  |  || ||||| || |||||  ||||||| |||||||| ||||| || || ||||||||||| ||||| |||||||||||||  |    |||||   ||||||||  |  | |   || |  ||  || |    || || || |  |   |   || |     |   | ||||
AGGAGAAGCTGGAAAAATTTATTTGCATACATGGGGCCTGGGTTTCTTGTTTCCATTGCATATATAGATCCAGGAAACTgtaagaacacactattcatgattttcttctgtaatga--aaggaaatctatttctgacatggtatacttatggta---ttctaatgataattggcag

upper sequence: GRMZM2G069198_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G44710.1 (Glycine max), 5'ss of exon 1
---AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaacggattcac--ttttcttcgattctcattgagtatttcccttccatctattgtgtattcttcacaaattttttggtgtgtcttgcag
   |  || || ||||| || |||||  ||||||| |||||||| ||||| || || ||||||||||| ||||| |||||||||||||  |    |||||   ||||||||  |  | |  |   || |   |  |    |  || || |  |   |   || ||    |  || ||||
CAGAGGAAAAGCTGGAAAAATTTATTTGCATACATGGGGCCTGGGTTTCTTGTTTCCATTGCATATATAGATCCAGGAAACTgtaagaacacactattcatgattttcttctgtaatgaaaggaaatctatttgac----acggtatacttatggta---ttcttatgataactggcag

upper sequence: GRMZM2G069198_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G02680.1 (Glycine max), 5'ss of exon 1
AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaacggat--tcacttttcttcgattctcattgag-tatttcccttccatctattgtgtattcttcacaaattttttggtgtgtcttgcag
| ||   | ||||| ||| ||||  ||||| | || ||||||||||| || || ||||||||||| || || |||||||||||||| |     |  |||||||  |  ||     |  ||  ||| | ||   |||  ||    |  |  |   |   ||||     || |||||||
ACAACAGGCTGGAAAAACCTATTTGCATACGTGGGACCTGGATTTCTAGTTTCCATTGCATATATCGACCCGGGAAACTgtaagatcacttattcatcactttcttctgaaagaaaaggaaatatattcccaacatagat---atgattattgta---ttttcaccttgacttgcag

upper sequence: GRMZM2G069198_T04 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA08G23320.1 (Glycine max), 5'ss of exon 3
AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaacggat--tcacttttcttcgattctcattgag-tatttcccttccatctattgtgtattcttcacaaattttttggtgtgtcttgcag
| ||  || ||||| ||||||||  ||||||| |||||||||||||| || || ||||||||||| || || |||||||||||||| |     |  |||||||  |  ||     |  ||  ||| | |||  |||  |     ||| |||  |  ||||||     || |||||||
AGAACAAGCTGGAAAAACTTATTTGCATACATTGGGCCTGGATTTCTTGTTTCCATTGCATATATCGACCCAGGAAACTgtaagatcatttattcatcactttattctgaaataaaaggaaatatattcctgacataga-----tatgcttatcgtatttttcacaatgacttgcag

upper sequence: GRMZM2G069198_T04 (Zea mays), 5'ss of exon 3
lower sequence: AT1G80830.1 (Arabidopsis thaliana), 5'ss of exon 2
AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaacggattcacttttcttc-gattctcattgagtatttcccttccatctattgtgtattcttcacaaattttttggtgtgtcttgcag
|| || || |||||||| || ||  | ||| |||| ||||| ||||| || ||||| |||||||||||||||||||||||||||   |      || ||||| ||   ||  ||  | |  ||||    |  ||  ||| |   ||||||         ||  |||||  |||||
AAGAAGAGCTGGAAGAATTTCTTTGCTTACTTAGGCCCTGGTTTTCTTGTTTCAATCGCATATATTGATCCTGGAAACTgtaagcacattactctctctttttttttaataatctgtaaagatttgagatg-attcattcttgtttcttc---------ttcctgtgttctgcag

upper sequence: GRMZM2G069198_T04 (Zea mays), 5'ss of exon 3
lower sequence: AT1G15960.1 (Arabidopsis thaliana), 5'ss of exon 2
AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaacggattcacttttcttcgattctcattgagtatttcccttccatctattg-tgtattcttcacaaattttttggtgt-gtcttgcag
||||| || ||||| ||||| ||||||||| |||| ||||||||||| ||||||||||| || ||||||||||||||||||||||||          || ||  |  ||        ||| |  | ||| |    |  |    |  ||   ||  ||| ||| ||| ||  | |||
AAAAAGAGCTGGAAAAACTTCTTCTCATACTTAGGCCCTGGATTTCTTGTCTCAATTGCTTACATTGATCCTGGAAACTgtaagatt----------ctctttgtaaataaatga-aagtgtaacacttacgcagacagacacaagctatgcatttttgttgttgttgttgtacag

upper sequence: GRMZM2G069198_T04 (Zea mays), 5'ss of exon 3
lower sequence: Vv09s0070g00210.t01 (Vitis vinifera), 5'ss of exon 3
AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaacggattcacttttcttcgattctcattgagtatttcccttccatctattgtgtattcttcacaaattttttggtgtgtcttgcag
|  || || ||||| ||||||||  |||| || || ||||| ||||| || || ||||||||||||||||||||||| ||||||| | |    |     || |||   ||   | |    | | | |||||    ||| ||   || ||  | ||||| || |  | |||||||
AGGAAAAGCTGGAAAAACTTATTTGCATATATGGGTCCTGGGTTTCTTGTGTCTATTGCATATATTGATCCTGGAAATTgtaagactgagacttcttagttcctttttttactactataaaatgctcttcc--taattatgccctcatc-tatattttgtgat-cgccttgcag

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|211420191|gb|FL124229.1|FL124229
EST:     CATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACT                         TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG
genomic: CATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaa ... tgtcttgcagTTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG
EST: gi|211420188|gb|FL124226.1|FL124226
EST:     CATAGGGCCTGGATTTCTCGTCTCAATTGCATAT-T-GATCCTGGAAACT                         TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG
genomic: CATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaa ... tgtcttgcagTTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG
EST: gi|211049303|gb|FL092984.1|FL092984
EST:     CATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACT                         TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG
genomic: CATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaa ... tgtcttgcagTTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG
EST: gi|211420190|gb|FL124228.1|FL124228
EST:     CATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACT                         TTGAGACGGATCTACAGGCTGGAG
genomic: CATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaa ... tgtcttgcagTTGAGACGGATCTACAGGCTGGAG
EST: gi|93014188|gb|EB639708.1|EB639708
EST:     CATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACT                         TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG
genomic: CATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaa ... tgtcttgcagTTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG
EST: gi|88757771|gb|DY541912.1|DY541912
EST:     CATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACT                         TTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG
genomic: CATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaa ... tgtcttgcagTTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG

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: 49 (upstream exon), 41 (downstream exon)
Score: 85

AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaa ... tgtcttgcagTTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 707

AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaa ... tgtcttgcagTTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 521

AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaa ... tgtcttgcagTTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 139

AAAAACAGTTGGAAGAACTTATTCTCATACATAGGGCCTGGATTTCTCGTCTCAATTGCATATATTGATCCTGGAAACTgtaagattaa ... tgtcttgcagTTGAGACGGATCTACAGGCTGGAGCACAGTACAAATATGAG