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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGATGGCGATGATGGCTATGCGACGCGCGGTGGCGCTCGGCGCTCGCCACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgcccccctcacatcatcaacccaccatcctctggccgcttcatagaacacccctaggccttcgccatcccgtcggcgcgtcactgtgcgggtttgatatattttgagtgtgcag

Basic information

species Zea mays
transcript GRMZM2G119482_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119482_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g07760.1 (Oryza sativa), 5'ss of exon 1
GGCGATGGCGATGATGGCTATGCGACGCGCGGTGGCGCTCGGCGCTCGCCACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgcccccctcacatcatcaacccaccatcctctggccgcttcatagaacacccctaggccttcgccatcccgtcggcgcgtcactgtgcgggtttgatatattttgagtgtgcag
|||||||||||||  |   ||||||||||||| |||||||||||| |||||||||| ||||||| |  || | || | |   | ||||  |||||||| |  |||  | |  |          ||| |   || |   || ||||  |           |||  | ||  |    | ||   ||   ||||| |                        
GGCGATGGCGATGGCG---ATGCGACGCGCGGCGGCGCTCGGCGCGCGCCACATCCTCGCCGCCTCGTCCACCTCCTCCTCCGGCGTCCTCCTCCGCCGC-CACgtactctcc----------ccctctgccccccccccccttcggatgtgggtttagggcgcttgctgtga-attgggaggtt--tgtgcag------------------------
















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|76286306|gb|DV025874.1|DV025874
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|148933161|gb|EC876801.2|EC876801
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|211223364|gb|FL262903.1|FL262903
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|76289708|gb|DV029276.1|DV029276
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|149102730|gb|EE188270.2|EE188270
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|211223367|gb|FL262906.1|FL262906
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTKCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|211223366|gb|FL262905.1|FL262905
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|211225422|gb|FL262911.1|FL262911
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|76921995|gb|DV168797.1|DV168797
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|149000791|gb|EE038015.2|EE038015
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|78093012|gb|DV521386.1|DV521386
EST:     CCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: CCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|71330637|gb|DR802090.1|DR802090
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|211223365|gb|FL262904.1|FL262904
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
EST: gi|211223363|gb|FL262902.1|FL262902
EST:     ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCAC                         ATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG
genomic: ACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTG

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: 87

GGCGATGGCGATGATGGCTATGCGACGCGCGGTGGCGCTCGGCGCTCGCCACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTGCTCAGGACGCAGGGGCTTATCGCTGGGCAGTGGGTGGACGCCTACGACG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 176

GGCGATGGCGATGATGGCTATGCGACGCGCGGTGGCGCTCGGCGCTCGCCACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTGCTCAGGACGCAGGGGCTTATCGCTGGGCAGTGGGTGGACGCCTACGACG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GGCGATGGCGATGATGGCTATGCGACGCGCGGTGGCGCTCGGCGCTCGCCACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTGCTCAGGACGCAGGGGCTTATCGCTGGGCAGTGGGTGGACGCCTACGACG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 96

GGCGATGGCGATGATGGCTATGCGACGCGCGGTGGCGCTCGGCGCTCGCCACATCCCCGCCGCCGCAGCCTCTTCGTTCCGAGTCGTCTCCCTCCGCCACgtacgccccc ... gagtgtgcagATGAGCGCGGACGCGGGCGCCGCGATGGAGAAGATCCGCGCCGCCGGGCTGCTCAGGACGCAGGGGCTTATCGCTGGGCAGTGGGTGGACGCCTACGACG