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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACTgttagtatcatcaacaaaattcttcttttctaaagctatgttcttttcttttattaatcatttggtcgccattctcttcag

Basic information

species Zea mays
transcript GRMZM2G082855_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082855_T04 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 5'ss of exon 11
AGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACTgttagtatcatcaacaaaa--ttcttcttttctaaagctatgttcttttcttttattaatcatttggtcgccattctcttcag
|||||| |||||||| || ||||| ||||| |||||| ||||||| ||||| || ||||| || || ||||||||||||||||||   | |  ||||| ||  || |   |   ||||| |||| | | |  | |   ||| || ||  ||||||
AGACCTGAGTGAGAACGAGCTGGTAGGGCCCATTCCTTCTATACTGGGCAATCTATCCTATACTGGAAAACTgttagtatcatcagtcagactttctttttcactgagattgctttcttctcttctctaacacctactgtcaccttttccttcag
















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|148940443|gb|EC885241.2|EC885241
EST:     GTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACT                         CTATTTACATGGCAACAAACTCACTGGACATATACCAC
genomic: GTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACTgttagtatca ... ttctcttcagCTATTTACATGGCAACAAACTCACTGGACATATACCAC
EST: gi|149079907|gb|EE168913.2|EE168913
EST:     GTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACT                         CTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGGAA
genomic: GTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACTgttagtatca ... ttctcttcagCTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGGAA
EST: gi|149079906|gb|EE168912.2|EE168912
EST:     GTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCCAACT                         CTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGG
genomic: GTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACTgttagtatca ... ttctcttcagCTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGG
EST: gi|148964982|gb|EC906062.2|EC906062
EST:     GTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACT                         CTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGGAA
genomic: GTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACTgttagtatca ... ttctcttcagCTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGGAA
EST: gi|101383199|gb|EB813654.1|EB813654
EST:     GTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACT                         CTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGGAA
genomic: GTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACTgttagtatca ... ttctcttcagCTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGGAA
EST: gi|148961185|gb|EE011900.2|EE011900
EST:     CCTACACAGGCAAACT                         CTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGGAA
genomic: CCTACACAGGCAAACTgttagtatca ... ttctcttcagCTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGGAA

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 434

AGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACTgttagtatca ... ttctcttcagCTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGGAACATGAGTAAACTTAGCTACCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 65

AGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACTgttagtatca ... ttctcttcagCTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGGAACATGAGTAAACTTAGCTACCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 296

AGACCTTAGTGAGAATGAACTGGTGGGGCCTATTCCTCCTATACTTGGCAACCTGTCCTACACAGGCAAACTgttagtatca ... ttctcttcagCTATTTACATGGCAACAAACTCACTGGACATATACCACCAGAACTGGGGAACATGAGTAAACTTAGCTACCT