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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcactccctctttctcagtctctgacatatacaaacggtgagcacgcacaagcactgactgaaagttaaacacatgattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGTGTGATTGCTATCATTGTTGTCAAG

Basic information

species Zea mays
transcript GRMZM2G330650_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G330650_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g25390.1 (Oryza sativa), 3'ss of exon 8
gcactccc---tctttctcagtctctgacatatacaaacggtga-gcacgcacaagcactgactgaaagttaaacacatgattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGTGTGATTGCTATCATTGTTGTCAAG
| || |||    || ||||   |     | |   |    | |   ||| |  || ||| |  |||||| || ||  |      ||||||||||| ||||||||||| || |||||||| || || ||||| ||||  ||||||||||| || |||||||| |||
gtacccccatccctctctcttccctctgcgtgcgcttgtgcttttgcatgtcca-gcagtacctgaaatttgaaatc-----cttgcagGTTGCAACTGACAAATGCATTATGGCATTGCTTTTTCTGATTGTTTGTGGTGTGATTGCAATTATTGTTGTTAAG
















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|21810005|gb|BQ668323.1|BQ668323
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTTCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|148991480|gb|EE032993.2|EE032993
EST:     ACTTCTCCCTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|33467215|gb|CF244264.1|CF244264
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|87157738|gb|DY402527.1|DY402527
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTTCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|60338704|gb|DN205677.1|DN205677
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|110510919|gb|EE019261.1|EE019261
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|7135591|gb|AW498164.1|AW498164
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTTCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|18166041|gb|BM335880.1|BM335880
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|149097830|gb|EE183757.2|EE183757
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|50334133|gb|CO529259.1|CO529259
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|89754547|gb|DY685289.1|DY685289
EST:     ACTTCTCCCTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|86468443|gb|DY234813.1|DY234813
EST:     AGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTTTTCCTGATCGTTTTGGGT
genomic: AGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|76286033|gb|DV025601.1|DV025601
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|71306394|gb|DR789339.1|DR789339
EST:     ACTTTTCCCTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
EST: gi|76913444|gb|DV165140.1|DV165140
EST:     ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAG                         GTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT
genomic: ACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGT

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), 47 (downstream exon)
Score: 68

ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGTGTGATTGCTATCATTGTTGTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGTGTGATTGCTATCATTGTTGTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 128

ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGTGTGATTGCTATCATTGTTGTCAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 130

ACAGAGCAAATGAAGAGAATTGGTAATGAGCTAGATACTGTCCACTTCTCACTGAAGAAAGCTAGCCAACTAGTGAAGGAGATTGGTCGCCAGgcactccctc ... gattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGTGTGATTGCTATCATTGTTGTCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaacggtgagcacgcacaagcactgactgaaagttaaacacatgattttgcagGTTGCGACTGACAAATGTATCATGGCATTCCTCTTCCTGATCGTTTTGGGTGTGATTGCTATCATTGTTGTCAAG
                      cactgac  putative branch site (score: 130)
                               aaagttaaa  TA-rich tract