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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAGgttgctgtgtttataatgatgttcatgattcagattttttccagtgaaattttaggccaaaaatgtgaaatttatttatttttcctcag

Basic information

species Zea mays
transcript GRMZM2G136803_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G136803_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g46790.1 (Oryza sativa), 5'ss of exon 15
GAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAGgt-------tgctgtgtttataatgatgttcatgattcagattttttccagtgaaattttaggccaaaaatgtgaaatttatttatttttcctcag
||||||||||| |||||||| |||||||||||  || | |||||||  || || |||| |||||||| |||||||||       |  |||   || ||  ||| ||    ||    ||||  |  |    |    ||| ||  |   ||| ||||   |||| |     ||
GAGGAGCTTCTTAGTGAAGGCCTATGGGATTTCGATAGAATGAGCCGCCCTTATATTCTTCAGGAAACACTGGAGgtttgtctttcttgttcctaaaacaatgatctatcttttttttttaacaggaaggaaaacagggcaccagcatgacattt--ctattctgttatag
















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|211541853|gb|FL147715.1|FL147715
EST:     GGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAG                         GAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAG
genomic: GGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAGgttgctgtgt ... ttttcctcagGAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAG
EST: gi|78091048|gb|DV519422.1|DV519422
EST:     GGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAG                         GAGAAGTTTGGATCCTTT
genomic: GGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAGgttgctgtgt ... ttttcctcagGAGAAGTTTGGATCCTTT
EST: gi|7145217|gb|AW506698.1|AW506698
EST:     GGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAG                         GAGAAGTTTGGATCCTCTTGGACAGTCATTGCAGCCAATTTTCTAAATGAG
genomic: GGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAGgttgctgtgt ... ttttcctcagGAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAG
EST: gi|211541851|gb|FL147713.1|FL147713
EST:     GGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAG                         GAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAG
genomic: GGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAGgttgctgtgt ... ttttcctcagGAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAG
EST: gi|211153097|gb|FL147716.1|FL147716
EST:     GGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAG                         GAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAG
genomic: GGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAGgttgctgtgt ... ttttcctcagGAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAG
EST: gi|78120827|gb|DV539211.1|DV539211
EST:     GGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAG                         GAGAAGTTTGGATCCTTTTGGACAGTCCTTGCAGCCAATTTTCTAAATGAG
genomic: GGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAGgttgctgtgt ... ttttcctcagGAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAG

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: 152

GAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAGgttgctgtgt ... ttttcctcagGAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 281

GAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAGgttgctgtgt ... ttttcctcagGAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAG


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

GAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAGgttgctgtgt ... ttttcctcagGAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 344

GAGGAGCTTCTAAGTGAAGGTCTATGGGATTTTAATCGGATGAGCCAACCATACATTCGTCAGGAAATACTGGAGgttgctgtgt ... ttttcctcagGAGAAGTTTGGATCCTTTTGGACAGTCATTGCAGCCAATTTTCTAAATGAGTACCAGAAGCAGTGTTATGAG