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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactacttcaatccagtgacgtaacctaattttgccctgtggggtgggaaggtagctgatcattgccttctgtatatcag

Basic information

species Zea mays
transcript GRMZM2G051004_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os02g07490.1 (Oryza sativa), 5'ss of exon 12
GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactacttc--aatccagtgacgtaacctaattttgccctgtggggtgggaaggtagc-tgatcattgccttctgtatatcag
||| ||||||||||||||||| ||||||||||| || |||||||| ||||| || ||||||||||| || ||||||||| | |||| | ||||||   ||  |  || ||||  |  | |||  ||     | | |  | |  | | |      | ||||| |||||||
GGCAGCATCAGAGGGTGCACTGAAAGGTATTCTAGGTTACACAGATGAGGATGTGGTTTCCAATGACTTCGTTGGTGATGCAAGgtaagtacttctagatgtaccgatgtaaattg-tgttgtgctcaaaagggagtggttgacataactgcccctttctgcatatcag

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA03G22790.1 (Glycine max), 5'ss of exon 12
GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtg-actac-ttcaatccagtgacgt----aacctaatt---ttgccctgtggggtgggaaggtagctgatcattgccttctgtatatcag----------
|   || ||||||||  |||| |||||||| ||||| |||||||||||||| ||||| || ||||| |||||||||||||| ||||    ||  |||       | || |    | | |   |   || |  |   || |||||||  ||   | ||| |        ||| |            
GTATGCCTCAGAGGGACCACTGAAAGGTATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAGgtacgttatgttctgctatattacctttaaagctttgctgaattactttcctggttgggaagtgagac-accatagaacctgagatacccagttggttgac

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA16G09020.1 (Glycine max), 5'ss of exon 12
GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtg-actacttcaatccagtgacgtaacctaa----ttttgc-------cctgtggggtgggaaggtagctgatcattgccttctgtatatcag------
|   || ||||||||  |||| ||||| || ||||| |||||||||||||| ||||| || ||||| |||||||||||||| ||||    ||  |   || | |  | | | |  |     |||||       | | |  ||| | || ||     | ||| |        ||| |        
GTATGCCTCAGAGGGACCACTGAAAGGAATCCTTGGGTACACAGACGAGGATGTTGTCTCTAATGACTTTGTTGGTGATTCAAGgtacgttatgttcttctattacctttaacggaaagactttgctgaattacttttctggttgaaaagtgagacaccatagaaactgacatacccagtttgg

upper sequence: GRMZM2G051004_T01 (Zea mays), 5'ss of exon 12
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 5'ss of exon 12
GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactacttcaatccagt--------gacgtaacc-----taattttg------ccctgtggggtgggaaggtagctgatcattgccttctgtatatcag-
|   || ||||||||  || | || ||||||||||| ||||| || ||||| ||||| |||||||||||||||||||| || ||||       ||||||   |        || |||| |     |||| |||      |  | |||| |    ||  | | |||  |  |||| ||| | | |  
GTATGCCTCAGAGGGGCCATTGAAGGGTATTCTTGGATACACGGATGAGGATGTTGTCTCCAATGATTTTGTTGGTGACTCAAGgtagaattctcaatctcataatcacttgatgtaatcggaattaatattgagtatactttctgggctccatag--aacggatagtgaccttgtgtttctaaaa

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|211015683|gb|FL453044.1|FL453044
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|211407297|gb|FL458695.1|FL458695
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|148928089|gb|EC872534.2|EC872534
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTTTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|37397668|gb|CF636141.1|CF636141
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|67025324|gb|CO454073.1|CO454073
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|40337147|gb|CK371217.1|CK371217
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|84977532|gb|DW475954.1|DW475954
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GCCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|30306629|gb|CD001302.1|CD001302
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|31997624|gb|CD661686.1|CD661686
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|148944446|gb|EC889561.2|EC889561
EST:     GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
EST: gi|6021812|gb|AW066740.1|AW066740
EST:     GGCTACCCAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTNTAG                         GTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT
genomic: GGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCAT

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), 48 (downstream exon)
Score: 35

GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG


Block sizes: 38 (upstream exon), 46 (downstream exon)
Score: 13

GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 10

GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 87

GGCGGCATCAGAGGGTGCACTCAAAGGTATTCTTGGCTACACAGACGAGGACGTTGTTTCCAATGATTTTGTTGGTGATTCTAGgtgactactt ... tgtatatcagGTCAAGCATCTTTGATGCCAAGGCTGGTATCGGACTGAGCTCTTCTTTCATGAAGCTTGTGTCTTGGTATGACAACGAGTGGGGCTACAG