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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtatttttgtcatgtgctcaataattaccttgatgttgcatatatgccaccatttttttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATCCTGTGTGGATGTGACTATTGTGATAGCATCAAAG

Basic information

species Zea mays
transcript GRMZM2G121262_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121262_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os05g46270.1 (Oryza sativa), 3'ss of exon 10
gtgtgtatttttgtcatgtgctcaataattaccttgatgttgcatatatgccacca-tttttttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATCCTGTGTGGATGTGACTATTGTGATAGCATCAAAG
|| || |    ||| || ||||   ||   ||  |||||||| | | |    |||| ||||  | ||| ||||||||||||||||||||||||| |||||||| |||||||| ||||||||||| | |||||||||||||||||||||||| ||||
gtatgcagcactgtgatttgcttggtacagacactgatgttgtacacacttgaccaattttcatattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATCCTATCTGGATGTGACTATTGTGATAGCATTAAAG

upper sequence: GRMZM2G121262_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT5G26680.2 (Arabidopsis thaliana), 3'ss of exon 10
gtgtgtatttt--------tgtcatgtgctcaata-attaccttgatgttgcatatatgccaccatttttttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATCCTGTGTGGATGTGACTATTGTGATAGCATCAAAG
|| ||| | |         | |  | |  ||||   ||||  || |||         |   |   |  | | |||  || |||| || |||||| |||| |||||||| |||||||| || ||||| ||  ||| |||||||||||||||||| ||||||  ||
gtttgtctctcacacacactattctttcttcaacgtattaagttaatgaactgatccttatattgtggtctcgtttcagATTTTAGAAGAGCTTCAACTTACCATGGATCAGTTCATCGACTTGTGTATATTGTCTGGATGTGACTATTGTGACAGCATCCGAG
















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|32800869|gb|CD953105.1|CD953105
EST:     GATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: GATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|88852819|gb|DY543043.1|DY543043
EST:     TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCATTTTATTGATTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|6695706|gb|AW288784.1|AW288784
EST:     TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGNTCATTGATTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|148983038|gb|EE028944.2|EE028944
EST:     TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|32789007|gb|CD941243.1|CD941243
EST:     GATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: GATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|78180993|gb|DV551366.1|DV551366
EST:     TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|148945123|gb|EC890320.2|EC890320
EST:     TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|148985934|gb|EE029847.2|EE029847
EST:     AAGAAAATACCTG-GATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: AAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|78117503|gb|DV535890.1|DV535890
EST:     TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|148985935|gb|EE029848.2|EE029848
EST:     TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|5847296|gb|AW000375.1|AW000375
EST:     TGGATCCAAGTTTCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|18661475|gb|BM501417.1|BM501417
EST:     GGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTT-GGAGGAGCCTT-AACTCA
genomic: GG-ATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGC-TTGAACTCA
EST: gi|71444731|gb|DR825781.1|DR825781
EST:     TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|74235361|gb|DT643275.1|DT643275
EST:     TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|93014006|gb|EB639526.1|EB639526
EST:     TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCCAG                         GTTTTGGAGGAGCTTGAACTCACCCTGGACCAGTTCATTGA
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGA
EST: gi|76018920|gb|DT946090.1|DT946090
EST:     TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|74235360|gb|DT643274.1|DT643274
EST:     AAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: AAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
EST: gi|60349759|gb|DN216732.1|DN216732
EST:     TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAG                         GTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATC

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: 48 (upstream exon), 49 (downstream exon)
Score: 484

AGATATGGACTCCCTTACTTTTGGGGCTCCACGGTTCCTTCGTCATTTAATGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATCCTGTGTGGATGTGACTATTGTGATAGCATCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 114

AGATATGGACTCCCTTACTTTTGGGGCTCCACGGTTCCTTCGTCATTTAATGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATCCTGTGTGGATGTGACTATTGTGATAGCATCAAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 103

AGATATGGACTCCCTTACTTTTGGGGCTCCACGGTTCCTTCGTCATTTAATGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATCCTGTGTGGATGTGACTATTGTGATAGCATCAAAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 57

AGATATGGACTCCCTTACTTTTGGGGCTCCACGGTTCCTTCGTCATTTAATGGATCCAAGTTCCAAGAAAATACCTGTGATGGAATTTGATGTTGCCAAGgtgtgtattt ... tttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATCCTGTGTGGATGTGACTATTGTGATAGCATCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtgctcaataattaccttgatgttgcatatatgccaccatttttttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATCCTGTGTGGATGTGACTATTGTGATAGCATCAAAG
                ccttgat  putative branch site (score: 57)
                                      ccattttttt  putative PPT
                                        atttttttgttgta  TA-rich tract