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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccctctttttgacgtagtcttcttgttgccattctttcttggagtatatgttgacatggtgttgtgacatttgcccttccacag

Basic information

species Zea mays
transcript GRMZM2G037698_T02
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037698_T02 (Zea mays), 5'ss of exon 17
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 15
GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccctctttt-tgacgta-------gtcttcttgttgccattctttcttggagtatatgttgacatggtgt-tgtgacatttgcccttccacag
||| ||||||||||| |||||||||   |||||||||||  ||||||| ||||||||||| || || ||||||  | |||| | || || |  |       |  |  |  ||| |||   | |||| | |  |   | |  |||| | |||| | |   |  |||  |||
GGTTTACCAAGTAGCAAATGTTAAGCTTGAATGGAATCTTGTCAAGACCTTACCAGATTTGTCAGGCACAGgttcgtccctttcttatggcccacattctcggttcgtgattggcatctgtgcttgcacttaac--taatttggtttctgtggcgtacacttttct-cag
















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|6022161|gb|AW067089.1|AW067089
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|32908360|gb|CF013173.1|CF013173
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAG
EST: gi|5055844|gb|AI734731.1|AI734731
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGG
EST: gi|32934237|gb|CF039049.1|CF039049
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTAC
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTAC
EST: gi|211272710|gb|FL005615.1|FL005615
EST:     ATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: ATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|20811259|gb|BQ295737.1|BQ295737
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|24764727|gb|CA399890.1|CA399890
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|211335935|gb|FL468899.1|FL468899
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|33090853|gb|CF050847.1|CF050847
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGT
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGT
EST: gi|32933281|gb|CF038093.1|CF038093
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGT
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGT
EST: gi|148987119|gb|EE030947.2|EE030947
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|8577012|gb|BE129649.1|BE129649
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAGGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|78024591|gb|DV492978.1|DV492978
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|32837457|gb|CD977135.1|CD977135
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGT
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGT
EST: gi|60341462|gb|DN208435.1|DN208435
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|24770079|gb|CA405208.1|CA405208
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|166410938|gb|EG060200.1|EG060200
EST:     CATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: CATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|5607968|gb|AI901635.1|AI901635
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|32936163|gb|CF040975.1|CF040975
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
EST: gi|33103734|gb|CF063694.1|CF063694
EST:     TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTAC
genomic: TAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTAC
EST: gi|30052202|gb|AI065491.2|AI065491
EST:     AATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAG                         GGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG
genomic: AATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAG

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: 46 (upstream exon), 47 (downstream exon)
Score: 67

GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAGGTTCTATGGACCGCAATCTACGGATATTTGGCCTCCCTGGAGACGACCA


Block sizes: 35 (upstream exon), 43 (downstream exon)
Score: 8

GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAGGTTCTATGGACCGCAATCTACGGATATTTGGCCTCCCTGGAGACGACCA


Block sizes: 37 (upstream exon), 43 (downstream exon)
Score: 7

GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAGGTTCTATGGACCGCAATCTACGGATATTTGGCCTCCCTGGAGACGACCA


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 20

GGTCTACCAAGTAGCTAATGTTAAGGCCGAATGGAATCTCATCAAGACATTACCAGATTTATCTGGAACAGgtatggccct ... ccttccacagGGAAAGTAACTTCGGTAAAGTTCGGAGCAGATGCTAAGTACATAGCCGTAGGTTCTATGGACCGCAATCTACGGATATTTGGCCTCCCTGGAGACGACCA