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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatactcatgagaaattgtgcatattttaaactggccagcctttttgcacttcgagccctaacccaactacaatgtgtggaaagtttgaaactgccagtctcatggttttttgttctgatattttttatttcaactcgtagTTACAAACTTGTCGTATCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCAACCATTTCTAATATCCAG

Basic information

species Zea mays
transcript GRMZM2G021784_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G021784_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g01180.1 (Oryza sativa), 3'ss of exon 3
gtaatactc--atgagaaattgtgcatattttaaactggccagcctttttgcacttcgagccctaacccaactacaatgtgtggaaagtttgaaactgccagtctcatggttttttgttctgatattttttatttcaactcgtagTTACAAACTTGTCGTATCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCAACCATTTCTAATATCCAG
|||||||    || |||||| | || || ||||    | |  || | || | ||||  | |         | || ||  ||       |   | |||||       ||| |   || || | || |  ||| | |  | | |||||||||| |||||||| ||  |  | || |||||||||||| ||||||| |||||||| |||||||||
gtaatacaagaataagaaatcgagcctactttagcgcgtctggcatgtt-gtactttcaac---------agtataacatg------atactacactgc-------atgttgccttcttttaatttcctttgtctgcatttgtagTTACAAGCTTGTCGTGTCTACGCCGGAACCTAGAAAAGTGGCATCTCCGACCATTTCAAATATCCAG
















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|21389954|gb|BQ528003.1|BQ528003
EST:     ATCCATAAAATTGCCTCCACAGGTCAACCAGCCTCTGCAACAACAGGAGG                         TTACAAACTTGTCGTATCCTCAGCAGAGCCTAGATAAGTGTCATCTCCAAC
genomic: ATCCATAGAATTGCCTCCACAGGTCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caactcgtagTTACAAACTTGTCGTATCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCAAC




















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: 52

CAGTGTACTTTGCTTTGCATGACGACAATCTTGATAACCTGCTGGCAGATATCCATAGAATTGCCTCCACAGGTCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caactcgtagTTACAAACTTGTCGTATCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCAACCATTTCTAATATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

CAGTGTACTTTGCTTTGCATGACGACAATCTTGATAACCTGCTGGCAGATATCCATAGAATTGCCTCCACAGGTCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caactcgtagTTACAAACTTGTCGTATCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCAACCATTTCTAATATCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 55

CAGTGTACTTTGCTTTGCATGACGACAATCTTGATAACCTGCTGGCAGATATCCATAGAATTGCCTCCACAGGTCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caactcgtagTTACAAACTTGTCGTATCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCAACCATTTCTAATATCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

CAGTGTACTTTGCTTTGCATGACGACAATCTTGATAACCTGCTGGCAGATATCCATAGAATTGCCTCCACAGGTCAACCAGCCTCTGCAACAACAGGAGGgtaatactca ... caactcgtagTTACAAACTTGTCGTATCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCAACCATTTCTAATATCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaactgccagtctcatggttttttgttctgatattttttatttcaactcgtagTTACAAACTTGTCGTATCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCAACCATTTCTAATATCCAG
                           ttctgat  putative branch site (score: 54)
                                   ttttttatttc  CT-rich tract
                    ttttttgttctgatat  TA-rich tract