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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acagactcaataagataccattatctcctatagacttaggtaattcttatacttataattcttctacctttaattttattgaactgtttgttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC

Basic information

species Zea mays
transcript GRMZM2G006130_T06
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006130_T08 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 10
acagactcaataagataccat-tatctcctatagacttaggtaattcttatacttataattcttctacctttaattttattgaactgtttgt-tttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC
||  |  ||| || ||||||  |||||  |    | ||  |  | | |  || |||| ||    | || |||  |||            ||| | ||||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||||| ||||  |||||| 
acctatccaagaaaataccaaatatcttttccttaattgag--actatggtagttatcataacaccacttttgttttgggaacgtctcctgtctctctacagGACGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCGACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCTGAACCATTCCCTGTCAAAT

upper sequence: GRMZM2G006130_T08 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os11g03730.3 (Oryza sativa), 3'ss of exon 10
acagactcaataagataccat-tatctcctatagacttaggtaattcttatacttataattcttctacctttaattttattgaa-----ctgtttgttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC
       ||| || |||| |  |||||  | | || ||    |  | |  ||||| |  |    | |  |||   |||    |       ||||   | ||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||||| |||||||| ||||||||||||||||| ||||| ||||  |||||| 
----taccaagaaaatactaaatatcttttcttgaattga--agctatgttacttgtcgtaacaccagttttttgtttgggaacatctcttgttgtctctctacagGACGTATTGGACAGTCTAGAATTTGCAAGGGGGAATGCAGATTCAACATGGGGTTCTGTTAGAGCTGCAATGGGGCACCCCGAACCATTCCCTGTCAAAT
















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|211221447|gb|FL389601.1|FL389601
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGGAGTGCAGATTCAACATG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGG-AGTGCAGATTCAACATG
EST: gi|87151803|gb|DY396592.1|DY396592
EST:     TAAGCCACAATGATGAAGTTGACACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|21331549|gb|BQ486930.1|BQ486930
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGTCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32929408|gb|CF034220.1|CF034220
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGCCAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32924613|gb|CF029425.1|CF029425
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|18963147|gb|BM660266.1|BM660266
EST:     TAAGCCACAATGATGAAGTTGACACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|18661865|gb|BM501621.1|BM501621
EST:     TAAGCCACAATGATGAAGTTGACACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32923839|gb|CF028651.1|CF028651
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|211150003|gb|FL374637.1|FL374637
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|211079656|gb|FL402147.1|FL402147
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGNCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|18654845|gb|BM499650.1|BM499650
EST:     TAAGCCACAATGATGAAGTTGACACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|20300152|gb|BQ163095.1|BQ163095
EST:     TAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32929966|gb|CF034778.1|CF034778
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32924017|gb|CF028829.1|CF028829
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32924051|gb|CF028863.1|CF028863
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32924183|gb|CF028995.1|CF028995
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32924623|gb|CF029435.1|CF029435
EST:     TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
EST: gi|32928349|gb|CF033161.1|CF033161
EST:     TAAGCCACAATGATGAAGTCGATACTGTAGCTATTGCCCCTTTTGTAAAG                         GATGTATTGGACAGTCTGGAATTTGCAAGGGGGAGTGCAGATTCAACATGG
genomic: TAAGCCACAATGATGAAGTTGATACTGTAGCTATTGCCCCTTTTGTAAAGgtatcttttt ... ttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatacttataattcttctacctttaattttattgaactgtttgttttctacagGATGTATTGGACAGTCTAGAATTTGCAAGGGGGAGTGCAGATTCAACATGGGGCTCTGTTAGGGCTGCAATGGGGCACCCTGAACCTTTCCTGGTCAAAC
                      ctttaat  putative branch site (score: 4)
                                         tttgttttct  putative PPT
       ttataattcttctacc  TA-rich tract