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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttcaacctcgagttcttcctgtgtgctgtactccttggggttctaagaatatcagttggtgctagcaaaaccaatggaacagaattattttgatactggttctatttgatatacatggatggattctttgtttaatatttaatgcaattgattttcaagtgcattgtccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATG

Basic information

species Zea mays
transcript GRMZM2G042074_T02
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042074_T02 (Zea mays), 3'ss of exon 21
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 26
gtttgtttc-aacctcgagttcttcctgtgtgctg--tactccttggggttctaagaatatcagttggtgctagcaaaaccaatggaacagaattattttgatactggttctatttgatatacatggatggattctttgtttaatatttaatgcaattgattttcaagtgcattgtccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATG
||| ||||  |||||| | || |   | |||  |   || |   ||     ||  |  | ||| |   |  |      |  | ||  |   ||| | |    |     | ||    |||   ||   ||  |||   | ||||||||  |  |||||| |  ||||  ||   ||||||| ||||||||| ||||| ||||||  |||||||||||||  |||| |  ||     | || || ||||||||||| ||| || |||||||||||| |||||| ||||
gttagtttttaacctccacttttatatttgtttttcctagtatatgtataccttggggtttcaataaatatttattggattagtg--atgaaatcagtggatttaatatactgagggatgatcac--ataaattaaatatttaatatgaaccgcaatttaacttcacatgtgctgtccacatgcagGAGAAAGCTTTAGCAGAGGCAGAAAATAGGCCGCTGCCCCAATCATTTTCAAGTAACGATGTCCGTGCCTTACGACTAAGTGATTTCAAACATGCTCATG
















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|60672183|gb|DN474952.1|DN474952
EST:     TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAG                         GAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
genomic: TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
EST: gi|32936435|gb|CF041254.1|CF041254
EST:     TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAG                         GAGAGAGCTTCAGCAGAAACAGAAAATAGGCCCTTGCCTCTGTCACACCCT
genomic: TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
EST: gi|211424429|gb|FK972466.1|FK972466
EST:     TGAAAAGGAGAAGAAG                         GAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
genomic: TGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
EST: gi|6828013|gb|AW331656.1|AW331656
EST:     TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAG                         GAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCCCCCT
genomic: TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
EST: gi|7238135|gb|AW573357.1|AW573357
EST:     TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAG                         GAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
genomic: TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
EST: gi|7227796|gb|AW566437.1|AW566437
EST:     TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAG                         GAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
genomic: TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
EST: gi|6536570|gb|AW224883.1|AW224883
EST:     TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAG                         GAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
genomic: TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
EST: gi|20506891|gb|BQ279387.1|BQ279387
EST:     TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAG                         GAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
genomic: TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
EST: gi|33096896|gb|CF056856.1|CF056856
EST:     TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAG                         GAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
genomic: TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
EST: gi|26456741|gb|CA828324.1|CA828324
EST:     TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAG                         GAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
genomic: TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
EST: gi|22819410|gb|BU499500.1|BU499500
EST:     TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAG                         GAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT
genomic: TTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACT

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: 133

AATCTTTGTGTTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118

AATCTTTGTGTTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 96

AATCTTTGTGTTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 222

AATCTTTGTGTTACTGCTGCTCATCGTCCTATTAGGGAGATTCTTGAAAAGGAGAAGAAGgtttgtttca ... ccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctttgtttaatatttaatgcaattgattttcaagtgcattgtccacctgcagGAGAGAGCTTCAGCAGAAACAGAAAATAGGCCATTGCCTCTGTCGCACACTAGCAATGATGTCCGTGCATTAAGAATAAGTGATTTCATACATGCGCATG
                       aattgat  putative branch site (score: 222)
                                            tccacct  putative PPT
     ttgtttaatatttaat  TA-rich tract