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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttcttctttgcacacatgaatcagcagtatttgacgtggaacttgcaacttgcgggtgcatcatgtactaatgttcatttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGCGTTCTGAACATTGCACCTGGTTCAGGACGATACGTCATGATGCCACCTT

Basic information

species Zea mays
transcript GRMZM2G020002_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G020002_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 15
gttggttcttctttgcacacatgaatcagcagtatttgacgtggaacttgcaacttgcgggtgcatcatgtactaatgttcatttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGCGTTCTGAACATTGCACCTGGTTCAGGACGATACGTCATGATGCCACCTT
|| ||| | || || | ||||        | | |||||      | |||| |     |   ||  |  | |     |  ||| |  |||||||||||||| ||| | || |||||||| || ||||| || |||||||||||| |||||||| |||  || ||||||||| |||||||||  |  || ||||
gtcggtccctcgttactcaca-------actgcatttgcaa--aagcttgaattcaacttatgttttctttttctct-ctcaatcggtgtagGGAATGGTAGAAGTCACGATCTCAAGAGGGCGAGTTGTGTGGGAGGATGGCATTCTGAACGTTGTTCCCGGTTCAGGAAGATACGTCAGAACACCGCCTT
















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|74240936|gb|DT648850.1|DT648850
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|149070477|gb|EE158879.2|EE158879
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGAGGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|113703820|gb|EE681324.1|EE681324
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|211361841|gb|FL432810.1|FL432810
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|32809720|gb|CD961954.1|CD961954
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|148990302|gb|EE031901.2|EE031901
EST:     CACCCCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|18176646|gb|BM351579.1|BM351579
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|78079711|gb|DV508123.1|DV508123
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|148929734|gb|EC876616.2|EC876616
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGAGGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
EST: gi|149082367|gb|EE171551.2|EE171551
EST:     CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAG                         GGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC
genomic: CACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGC

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), 43 (downstream exon)
Score: 10

AGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGTGCTCTCACACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGCGTTCTGAACATTGCACCTGGTTCAGGACGATACGTCATGATGCCACCTT


Block sizes: 49 (upstream exon), 28 (downstream exon)
Score: 22

AGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGTGCTCTCACACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGCGTTCTGAACATTGCACCTGGTTCAGGACGATACGTCATGATGCCACCTT


Block sizes: 48 (upstream exon), 37 (downstream exon)
Score: 16

AGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGTGCTCTCACACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGCGTTCTGAACATTGCACCTGGTTCAGGACGATACGTCATGATGCCACCTT


Block sizes: 46 (upstream exon), 31 (downstream exon)
Score: 6

AGATATCATAATCCTGAACCCTGAAAGGAGCTTTGTGATGGGTGCTCTCACACACCATTCGAGGTCCAACACCAATGTGTACGAGGGCAGGAAAGGAAAGgttggttctt ... tttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGCGTTCTGAACATTGCACCTGGTTCAGGACGATACGTCATGATGCCACCTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacgtggaacttgcaacttgcgggtgcatcatgtactaatgttcatttcgtgtagGGAATGGTGGAAATAACAATCTCAAGGGGCCGAGTGGTATGGGAGGATGGCGTTCTGAACATTGCACCTGGTTCAGGACGATACGTCATGATGCCACCTT
                                 tactaat  putative branch site (score: 6)
                                         ttcatttc  CT-rich tract
                                 tactaat  TA-rich tract