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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttctattttatgacattatcttttgtaatttttttccattttaacctctcatcatgtgtttcttatttcatttttcttgtttagATTTATGCTGCAGAAACTTTATGCTCTGGTAGATCAAACTGCTTCACCTGACAATCCCGACGCGCTACAATACCAGGAGGCTCTATTGCCTGGGCACTTA

Basic information

species Zea mays
transcript GRMZM2G388892_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G388892_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os10g35290.1 (Oryza sativa), 3'ss of exon 8
gtgagtttctattttatgacattatcttttgtaatttttttccattttaacctctc--atcatgtgtttcttatttcatttttc-ttgtttagATTTATGCTGCAGAAACTTTATGCTCTGGTAGATCAAACTGCTTCACCTGACAATCCCGACGCGCTACAATACCAGGAGGCTCTATTGCCTGGGCACTTA
|| ||||    ||||||  |  | |  | || ||||| | ||| ||| |||||||   || |||||| |||  | | | |||||  |  ||||||||||||||||||||||||||||  | |||||||||||||| |||||||| ||  | || || ||||| |||||||| | ||| |||||||| ||| | 
gtaagttgaagttttattgctcttttctgtg-aatttctatccttttgaacctctttaatgatgtgtatctcttattacttttcacttcttagATTTATGCTGCAGAAACTTTATGCGATTGTAGATCAAACTGCGTCACCTGATAAAGCTGATGCTCTACAGTACCAGGAAGTTCTCTTGCCTGGCCACCTG
















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|33095197|gb|CF055191.1|CF055191
EST:     TATATTTTTGTGCACTTGGAAAATAACCATGATAAATTTAATCTATTGAT                         ATTTATGCTGCAGAAACTTTATGCTCTGGTAGATCAAACTGCTTCACCTGA
genomic: TATATTTTTGTGCACTTGGAAAATAACCATGATAAATTTAATCTATTGATgtgagtttct ... tcttgtttagATTTATGCTGCAGAAACTTTATGCTCTGGTAGATCAAACTGCTTCACCTGA




















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: 91

GTTGCTGAAGCGGTTCTAAAGGACTATATTTTTGTGCACTTGGAAAATAACCATGATAAATTTAATCTATTGATgtgagtttct ... tcttgtttagATTTATGCTGCAGAAACTTTATGCTCTGGTAGATCAAACTGCTTCACCTGACAATCCCGACGCGCTACAATACCAGGAGGCTCTATTGCCTGGGCACTTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 39

GTTGCTGAAGCGGTTCTAAAGGACTATATTTTTGTGCACTTGGAAAATAACCATGATAAATTTAATCTATTGATgtgagtttct ... tcttgtttagATTTATGCTGCAGAAACTTTATGCTCTGGTAGATCAAACTGCTTCACCTGACAATCCCGACGCGCTACAATACCAGGAGGCTCTATTGCCTGGGCACTTA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 25

GTTGCTGAAGCGGTTCTAAAGGACTATATTTTTGTGCACTTGGAAAATAACCATGATAAATTTAATCTATTGATgtgagtttct ... tcttgtttagATTTATGCTGCAGAAACTTTATGCTCTGGTAGATCAAACTGCTTCACCTGACAATCCCGACGCGCTACAATACCAGGAGGCTCTATTGCCTGGGCACTTA


Block sizes: 47 (upstream exon), 39 (downstream exon)
Score: 30

GTTGCTGAAGCGGTTCTAAAGGACTATATTTTTGTGCACTTGGAAAATAACCATGATAAATTTAATCTATTGATgtgagtttct ... tcttgtttagATTTATGCTGCAGAAACTTTATGCTCTGGTAGATCAAACTGCTTCACCTGACAATCCCGACGCGCTACAATACCAGGAGGCTCTATTGCCTGGGCACTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttccattttaacctctcatcatgtgtttcttatttcatttttcttgtttagATTTATGCTGCAGAAACTTTATGCTCTGGTAGATCAAACTGCTTCACCTGACAATCCCGACGCGCTACAATACCAGGAGGCTCTATTGCCTGGGCACTTA
         ttttaac  putative branch site (score: 30)
                             tttcttatttcatttt  putative PPT
                                 ttatttcatttttctt  TA-rich tract