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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttttcgcttctgctacacaagttttggaggtcctagtatttaaggttttggatgtatcgagaggtttatttgtgtctctgtgtggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCC

Basic information

species Zea mays
transcript GRMZM2G157310_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157310_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g44660.1 (Oryza sativa), 3'ss of exon 2
-------------------gtacgttttcgcttctgctacac------aagttttggagg-tcctagtatttaaggttttggatgtatcgagaggtttatttgtgtctctgtgtggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCC
                    |||  | ||   | || | | |      || ||   | || |  |   ||||  | ||   |     | ||||||| ||| ||||| | ||||    || |||| ||||||||  |||| ||||| |||||||||||||||||||||||||| || | | |||   |||||||||||||||||||||||||||||||||||||
gtatgggtgctcttcgcttctacagtctctagtttgattcgcttgatgaaattccagtggcttttgacatttttgtttggagggagtttgagaggtgtatgtgtgtttatgtg---gtggtagGCAGCCATGGGTTGCTGAGGCAGGGGAACGAGGAGTACGACGCCAAGAGGGAGGAGCTGTTCGAGCACTACCACCCCATCGAGATCTGCCCCGACATCCC
















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|28566667|gb|CB278315.1|CB278315
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|101386461|gb|EB815247.1|EB815247
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|5268576|gb|AI770540.1|AI770540
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTCAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|76293679|gb|DV033247.1|DV033247
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|101385767|gb|EB814932.1|EB814932
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|9951997|gb|BE638580.1|BE638580
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTCAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|74242168|gb|DT650082.1|DT650082
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|78092209|gb|DV520583.1|DV520583
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|211095811|gb|FL316687.1|FL316687
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTCAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|211143628|gb|FL314871.1|FL314871
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTCAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|91048046|gb|EB158464.1|EB158464
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|91050984|gb|EB161402.1|EB161402
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|31354764|gb|CD439121.1|CD439121
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|71438827|gb|DR819877.1|DR819877
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|50333544|gb|CO528670.1|CO528670
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
EST: gi|71449422|gb|DR830472.1|DR830472
EST:     CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGA                         GTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG
genomic: CTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAG

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: 58

GTTATCGCCGACTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCC


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 46

GTTATCGCCGACTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 36

GTTATCGCCGACTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 40

GTTATCGCCGACTTCGATGGCACGCTCACGCGGTACTGGTACGACGGCGCCCGCGGGCAGAgtacgttttc ... tggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaaggttttggatgtatcgagaggtttatttgtgtctctgtgtggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCC
                           tttatttgt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttttcgcttctgctacacaagttttggaggtcctagtatttaaggttttggatgtatcgagaggtttatttgtgtctctgtgtggatgctagGTAGCCATGGACTGCTTAGGCAAGGGAACGAGGAGTACGACGCCAAGAGAGAAGCGTTGTATCAGCACTACCACCCCATCGAGATCTGCCCCGACATCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC