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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagagactaaggggtcttgctatccattgtggtgccacagtttattcgatcttttactgtctcattcatctaaaggatacatattcatcacagGTTGCTAGAAAAATGAAGGATGAAGAGGGATTTTACTATCCACACAACCTTGATTTTAGAGGTCGGGCTTATCCAATGCACCCTTATCTGAACCATTTGG

Basic information

species Zea mays
transcript GRMZM2G381395_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G381395_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os09g07120.1 (Oryza sativa), 3'ss of exon 8
gtaagagactaaggggtcttgctatccattgtggtgccacagtttattcgatcttttactgtctcattcatctaaaggatac--atattcatcacagGTTGCTAGAAAAATGAAGGATGAAGAGGGATTTTACTATCCACACAACCTTGATTTTAGAGGTCGGGCTTATCCAATGCACCCTTATCTGAACCATTTGG
|||||||||||    |  |  | |||                |||| ||  |   || ||       |||||||| | ||||  || ||  | |||||| ||| | ||||||||||||||||| || || ||||||||||||||||||||||||||||| || |||||||||||||| ||||| |||||||| ||||
gtaagagactataacgggtaaccatc---------------atttactcacttcattgct-------tcatctaatgaatactcatgttggtaacagGTAGCTCGCAAAATGAAGGATGAAGATGGTTTCTACTATCCACACAACCTTGATTTTAGAGGCCGTGCTTATCCAATGCATCCTTACCTGAACCACTTGG
















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|32931335|gb|CF036147.1|CF036147
EST:     AGAACAGTGAAAGGCATTCTCAGAGATGTGATGTTGAACTCAAACTTGCT                         GTTGCTAGAAAAATGAAGGATGAAGAGGGATTTTACTATCCACACAACCTT
genomic: AGAACAGTGAAAGGCATTCTCAGAGATGTGATGTTGAACTCAAACTTGCTgtaagagact ... ttcatcacagGTTGCTAGAAAAATGAAGGATGAAGAGGGATTTTACTATCCACACAACCTT




















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), 46 (downstream exon)
Score: 179

TGAAACCTTGCTAAAGAACTGGAAATGGCACTTGAGGGCAGCCAAGAAGAAGAACAGTGAAAGGCATTCTCAGAGATGTGATGTTGAACTCAAACTTGCTgtaagagact ... ttcatcacagGTTGCTAGAAAAATGAAGGATGAAGAGGGATTTTACTATCCACACAACCTTGATTTTAGAGGTCGGGCTTATCCAATGCACCCTTATCTGAACCATTTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 51

TGAAACCTTGCTAAAGAACTGGAAATGGCACTTGAGGGCAGCCAAGAAGAAGAACAGTGAAAGGCATTCTCAGAGATGTGATGTTGAACTCAAACTTGCTgtaagagact ... ttcatcacagGTTGCTAGAAAAATGAAGGATGAAGAGGGATTTTACTATCCACACAACCTTGATTTTAGAGGTCGGGCTTATCCAATGCACCCTTATCTGAACCATTTGG


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

TGAAACCTTGCTAAAGAACTGGAAATGGCACTTGAGGGCAGCCAAGAAGAAGAACAGTGAAAGGCATTCTCAGAGATGTGATGTTGAACTCAAACTTGCTgtaagagact ... ttcatcacagGTTGCTAGAAAAATGAAGGATGAAGAGGGATTTTACTATCCACACAACCTTGATTTTAGAGGTCGGGCTTATCCAATGCACCCTTATCTGAACCATTTGG


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 78

TGAAACCTTGCTAAAGAACTGGAAATGGCACTTGAGGGCAGCCAAGAAGAAGAACAGTGAAAGGCATTCTCAGAGATGTGATGTTGAACTCAAACTTGCTgtaagagact ... ttcatcacagGTTGCTAGAAAAATGAAGGATGAAGAGGGATTTTACTATCCACACAACCTTGATTTTAGAGGTCGGGCTTATCCAATGCACCCTTATCTGAACCATTTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttattcgatcttttactgtctcattcatctaaaggatacatattcatcacagGTTGCTAGAAAAATGAAGGATGAAGAGGGATTTTACTATCCACACAACCTTGATTTTAGAGGTCGGGCTTATCCAATGCACCCTTATCTGAACCATTTGG
                             atctaaa  putative branch site (score: 78)
                                      atacatatt  TA-rich tract