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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttcttactgatgatatgcaaatcattattctactccttacttcagtatttcttgtttagagactgaaataggtaaccttcatgaccagctaatt...

Basic information

species Zea mays
transcript GRMZM2G406603_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G406603_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G08060.2 (Glycine max), 5'ss of exon 5
CCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttcttactgatgatatgcaaatcattattctactccttacttcagtatttcttgtttagagactgaaataggtaaccttcatgaccagctaatt
||| | |||  |||||| ||||| |||||||||||||| ||||| || |||||||  |||||||| |||||| ||||||   |  |  ||| | |||||  | |  | |||  |  | ||| | | |     |  |||||   |   | |   |               
CCTAGGTGGAGTGATCTAGATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAGgtatttttct--gttcttgtattctaatca--actgcaatcc--atgttagt-tctttaaccaaaggactgtcttt--tgattgttgcag----------

upper sequence: GRMZM2G406603_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA05G08060.3 (Glycine max), 5'ss of exon 5
-------------------------------CCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttcttactgatgatatgcaaatcattattctactccttacttcagtatttcttgtttagagactgaaataggtaaccttcatgaccagctaatt
                               ||| | |||  |||||| ||||| |||||||||||||| ||||| || |||||||  |||||||| |||||| ||||||   |  |  ||| | |||||  | |  | |||  |  | ||| | | |     |  |||||   |   | |   |               
TTAGTTTACATAATGCATCTTCATTTTGCAGCCTAGGTGGAGTGATCTAGATATCAATCAGCATGTCAACAATGTGAAGTACATTGGCTGGATTCTGGAGgtatttttct--gttcttgtattctaatca--actgcaatcc--atgttagt-tctttaaccaaaggactgtcttt--tgattgttgcag----------

upper sequence: GRMZM2G406603_T02 (Zea mays), 5'ss of exon 6
lower sequence: GLYMA17G12940.2 (Glycine max), 5'ss of exon 6
CCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttcttactgatgatatgcaaatcattattctactccttacttcagtatttcttgtttagagactgaaataggtaaccttcatgaccagctaatt
 || | |||  |||||| ||||| |||||||||||||| ||||| || |||||||  |||||||| |||||| ||||||   |  |  ||| | ||||   | |  | |||||  ||   | ||  |     |  |||||   |  | |   ||               
TCTAGGTGGAGTGATCTAGATATCAATCAGCATGTCAACAATGTGAAGTACATTGACTGGATTCTGGAGgtatttttct--gttcttgtattctaatc--cactgcagtccttgttt---tgttgttaaccaaaggactgtcctttg-attgtttgcag----------

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|32869619|gb|CF009301.1|CF009301
EST:     ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG                         AGCGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
EST: gi|166466077|gb|EG135583.1|EG135583
EST:     ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG                         AGCGCACCCATCTC
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTC
EST: gi|71327050|gb|DR800172.1|DR800172
EST:     AATCAGCATGTCAATAATGTTAAATACATTGCGTGGGTTCTTGAG                         AGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: AATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
EST: gi|24773338|gb|CA408592.1|CA408592
EST:     ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATCCTTGAG                         AGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
EST: gi|5915436|gb|AW053077.1|AW053077
EST:     ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG                         AGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
EST: gi|211441828|gb|FL296923.1|FL296923
EST:     ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG                         AGCGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
EST: gi|24961561|gb|CA483567.1|CA483567
EST:     ATATAAATCAGCATGTCAATAATGCTAAATACATTGCGCGGATCCTTGAG                         AGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
EST: gi|60356288|gb|DN223261.1|DN223261
EST:     ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAG                         AGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG
genomic: ATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTG

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), 46 (downstream exon)
Score: 19

CCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTGGATTACAAAAGGGAGTGTGGCCGGGATAGTGTGCTGCAATCACACACCT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 38

CCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTGGATTACAAAAGGGAGTGTGGCCGGGATAGTGTGCTGCAATCACACACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 15

CCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTGGATTACAAAAGGGAGTGTGGCCGGGATAGTGTGCTGCAATCACACACCT


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

CCTCGTTGGGCTGATCTTGATATAAATCAGCATGTCAATAATGTTAAATACATTGCGTGGATTCTTGAGgtaattttct ... tttgcttcagAGTGCACCCATCTCTATTCTTGAGAATCATGAGCTGGCGAGCATTGTGCTGGATTACAAAAGGGAGTGTGGCCGGGATAGTGTGCTGCAATCACACACCT