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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaattgttctgctctttctaccatccagtctgctttcatggctatactttacttttactgtgcagatgtcaagaatacacacttgataccatgcttacctgttcataacaagatcagcagctgttcacatactgagtgtcgctatttctgactgttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCAGAGG

Basic information

species Zea mays
transcript GRMZM2G079538_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079538_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g32330.1 (Oryza sativa), 3'ss of exon 7
gtaaattgttctgctctttctaccatccagtctgctttcatggctatactttacttttactgtgcagatgtcaagaatacacacttgataccatgcttacctgttcataacaagatcagcagctgttcacatactgagtgtcgctatttctgactgttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCAGAGG
                                                                     || || || |   || |  |  ||  |||  ||| |     ||   |||        ||  |  ||   | |   |  |  || || | |||| ||| |||||||||| ||||| || || |||||||||||||| |||||||| |||||||| ||||||||   ||| |||||||||||||||||||| || ||||
---------------------------------------------------------------------gtgaaaaacattgacct--tctca-acttggctgctttcgcca---tcatatttcactccgaagcta--tttttttgatcgtgcct-tggtttccagTTCATTGCTAGCGAAGGTGATACTGTTACTCCAGGCACCAAAGTTGCTATCATATCAAAGTCTGCGGCACCAGCTGAAACACATGTTGCTCCGTCTGAGG
















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|5343075|gb|AI795485.1|AI795485
EST:     GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAGgtaaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|149074999|gb|EE163468.2|EE163468
EST:     GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAGgtaaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|32808216|gb|CD960450.1|CD960450
EST:     GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAGgtaaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|7145229|gb|AW506710.1|AW506710
EST:     GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAGgtaaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
EST: gi|29576970|gb|CB617082.1|CB617082
EST:     GTCACTATAGATGTCGCAAGTCCTGAGGCTGGAGTTATTGAAAAG                         CTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC
genomic: GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAGgtaaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATC

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: 45 (upstream exon), 49 (downstream exon)
Score: 231

GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAGgtaaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCAGAGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 351

GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAGgtaaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCAGAGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 300

GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAGgtaaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCAGAGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 431

GTCACTATAGATGTCGCAAGTCCTGAGGCTGGTGTTATTGAAAAGgtaaattgtt ... ttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCAGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatcagcagctgttcacatactgagtgtcgctatttctgactgttgtttacagCTCATTGCTAGTGAAGGCGACACAGTTACTCCAGGCACTAAAGTTGCAATCATATCCAAGTCTGCTCAACCTGCTGAAACACATGTTGCTCCATCAGAGG
                                    ttctgac  putative branch site (score: 431)
                                 tatttct  TA-rich tract