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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttggttgaatgaatattctgtgttctattcagaaaattctgacagccaaatttcctaataattatgaatgatcttttcttcctttcttgcaattcccacaaacagATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCT

Basic information

species Zea mays
transcript GRMZM2G106140_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G106140_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os05g37120.2 (Oryza sativa), 3'ss of exon 7
gtatgcttggttgaatgaatattctgtgttcta------ttcaga-aaattctgacagccaaatttcctaataattatgaatgatcttttcttcctttcttgcaattcccacaaacagATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCT
||  ||||| | |  ||  | |  | | || |       ||||   ||||||      |||||||| || ||    |||||||  |||| |  | |   ||||  || || | |||||||| |||||| | ||| ||||||| ||||||||||||||||||||| ||||||||||||||||||||||||| |||||||||
gtgagcttgatcgtttgtttgtcttttttttttctgcacttcattcaaattccatattccaaattttctgatccacatgaatggcctttgccccttggtttgccttttcctctaacagATATCGCTTATTGAGTAGACCCTATGCATTTGGTTGTGTTCTAAGGTTGAGAACATCTTCAGATTTTGAACCTGGCAATTCT
















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|71314648|gb|DR793946.1|DR793946
EST:     TATCTATTTCTCTATGCAAATGCAGATGATTCAACACTTCCTCAAGACAT                         ATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAG
genomic: TATCTATTTCTTTATGCAAATGCAGATGATTCAACACTTCCTCAAGACATgtatgcttgg ... ccacaaacagATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAG




















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), 49 (downstream exon)
Score: 107

AATACACGGATTTGGCTTCACTGAAGTTTTTAAGTATTGAAAGTGGTGGATATCTATTTCTTTATGCAAATGCAGATGATTCAACACTTCCTCAAGACATgtatgcttgg ... ccacaaacagATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 127

AATACACGGATTTGGCTTCACTGAAGTTTTTAAGTATTGAAAGTGGTGGATATCTATTTCTTTATGCAAATGCAGATGATTCAACACTTCCTCAAGACATgtatgcttgg ... ccacaaacagATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

AATACACGGATTTGGCTTCACTGAAGTTTTTAAGTATTGAAAGTGGTGGATATCTATTTCTTTATGCAAATGCAGATGATTCAACACTTCCTCAAGACATgtatgcttgg ... ccacaaacagATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

AATACACGGATTTGGCTTCACTGAAGTTTTTAAGTATTGAAAGTGGTGGATATCTATTTCTTTATGCAAATGCAGATGATTCAACACTTCCTCAAGACATgtatgcttgg ... ccacaaacagATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctaataattatgaatgatcttttcttcctttcttgcaattcccacaaacagATACCGCTTACTAAGTCGACCCTACGCATTTGGTTGTGTTCTAAGGCTGAGAACATCTTCAGATTTTGAACCAGGCAATTCT
  tcctaat  putative branch site (score: 205)
                     tcttttcttcctttct  putative PPT
     taataattatgaatga  TA-rich tract