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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtctattctgtgagttgtttgtttttcagtccagttatatttaatgataattttgttctctccatactaatcttttgatgttttattatgtctctggcag

Basic information

species Zea mays
transcript GRMZM2G553314_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 5'ss of exon 12
AGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcg---tctattctgtgagttgtttgtttttcagtccagttatatttaatgataattttgttctctccatactaatcttttgatgttttattatgtctctggcag
| |||||||| || ||||||||||||||||| ||||| || ||||||||||||||||| |||||||||||||||||||||||||||||||||||||||| ||      | || |||| ||||||  ||| | |  | | ||  ||  | | |  | | |  |   |  | || |  ||| |||||    ||| |  || | |   
AATTGCCTCTCCGGATGGCTGATTTTGGAGTCCTTCACAGGAATGAGCTTAGTGGTGCACTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaatgctaatgttgttttgtgggttgttaatttct-atactaattcaatccagttagtaatctccttgtttta-acca--cttctgatgc---attttccctgtag---
















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|211046688|gb|FL336954.1|FL336954
EST:     AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCTCATATCTTCTGCAGAGAAGACCAA
genomic: AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA
EST: gi|67033102|gb|CO461851.1|CO461851
EST:     AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCTCATATCTTCTGCAGAGAAGACCAA
genomic: AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA
EST: gi|22545540|gb|BU097899.1|BU097899
EST:     AGCTTAG-GGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCTCATATCTTCTGCAGAGAAGACCAA
genomic: AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA
EST: gi|211403724|gb|FL311348.1|FL311348
EST:     AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTARAAGATTCCAGCAG                         GATGATGCTCATATCTTCTGCAGAGAAGACCAA
genomic: AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA
EST: gi|211181488|gb|FL345837.1|FL345837
EST:     AGCTTAGTGGTACTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCTCATATCTTCTGCAGAGAAGACCAA
genomic: AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA
EST: gi|32832310|gb|CD971988.1|CD971988
EST:     AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCTCATATCTTCTGCAGAGAAGACCAA
genomic: AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA
EST: gi|211197538|gb|FL314132.1|FL314132
EST:     AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCTCATATCTTCTGCAGAGAAGACCAA
genomic: AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA
EST: gi|32834031|gb|CD973709.1|CD973709
EST:     AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCTCATATCTTCTGCAGAGAAGACCAA
genomic: AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA
EST: gi|50324858|gb|CO519984.1|CO519984
EST:     AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCTCATATCTTCTGCAGAGAAGACCAA
genomic: AGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA
EST: gi|20802797|gb|BQ293847.1|BQ293847
EST:     GTTTGACACGTGTTAGAAGATTCCAGCAG                         GATGATGCTCATATCTTCTGCAGAGAAGACCAA
genomic: GTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA

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), 49 (downstream exon)
Score: 299

AGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

AGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 222

AGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 145

AGTTGCCTCTTCGCATGGCTGATTTTGGAGTGCTTCATAGAAATGAGCTTAGTGGTGCTCTTACAGGTTTGACACGTGTTAGAAGATTCCAGCAGgtaaggcgtc ... tctctggcagGATGATGCTCATATCTTCTGCAGAGAAGACCAA