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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcaggtttctttagctaggattcgagtgagaagatgataaaactttattggtaatgtgtgccttatgcagatcctgtacaatatctactgagttttcttctaatccttttttatggttcgttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCCCTTGTTGGTATTGTG

Basic information

species Zea mays
transcript GRMZM2G160504_T01
intron # 13
splice site 3'
intron type U2

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|19769428|gb|BQ034149.1|BQ034149
EST:     CTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG                         GATAACATTTCACAGGATTCTAACTCGTACTACATCTTAACAATGATCTCC
genomic: CTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCC
EST: gi|78120836|gb|DV539220.1|DV539220
EST:     CTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG                         GATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCC
genomic: CTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCC
EST: gi|19769435|gb|BQ034156.1|BQ034156
EST:     CTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAG                         GATAACATTTCACAGGATTCTAACTCGTGCTACATCTTAGCAATGATCTCC
genomic: CTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCC

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: 44 (upstream exon), 47 (downstream exon)
Score: 13

ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCCCTTGTTGGTATTGTG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 51

ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCCCTTGTTGGTATTGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 61

ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCCCTTGTTGGTATTGTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 39

ATTTCTACCTCTGGCATGACTCTATGCCTTCTTGCCGTTTCTGTTGTATTTTTTCTCAAGgtatgttcag ... ttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCCCTTGTTGGTATTGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacaatatctactgagttttcttctaatccttttttatggttcgttttttccagGATAACATTTCACAGGATTCTAACTCATACTACATCTTAACAATGATCTCCCTTGTTGGTATTGTG
                      ttctaat  putative branch site (score: 39)
                                         ttcgttttttcc  putative PPT
                         taatccttttttat  TA-rich tract