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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcaccgcttgcttcaatttttaatgacaggagtgttaagaaactttgaatggactaacaatttttttcctctcccattagTGGTGGTGAACCAGAAAAGCCATTGGTAATACATGTGGGTCGTTTTGGACGTGAAAAAAATTTGGATTTTCTGAAAAG

Basic information

species Zea mays
transcript GRMZM2G049190_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G049190_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os03g15840.1 (Oryza sativa), 3'ss of exon 8
gtatcaccgcttgcttcaatttttaatgacagga-gtgttaagaaactttgaatgg---actaacaatttttttcctctcccattagTGGTGGTGAACCAGAAAAGCCATTGGTAATACATGTGGGTCGTTTTGGACGTGAAAAAAATTTGGATTTTCTGAAAAG
|| | |||  || ||| ||| || |||  ||| | |||  || ||| | || || |   ||| |   |  |||| |||||   |||||||||||||||||||||| ||| |  ||||||||||||||||||| || |||||||| ||||||||||||||||||||
gtttgacctatttctttaatattcaatagcagtatgtgaaaaaaaattgtgcatagctaacttattttcctttttctctcttgttagTGGTGGTGAACCAGAAAAACCACTCATAATACATGTGGGTCGTTTCGGGCGTGAAAAGAATTTGGATTTTCTGAAAAG
















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|71300886|gb|DR786473.1|DR786473
EST:     GAAAGCTTTCATACTAAATATCGGAGGCATGAAATGCGTGTCAGATTGAG                         TGGTGGTGAACCAGAAAAGCCATTGGTAATACATGTGGGTCGTTTTGGACG
genomic: GAAAGCTTTCATACTAAATATCGGAGGCATGAAATGCGTGTCAGATTGAGgtatcaccgc ... ctcccattagTGGTGGTGAACCAGAAAAGCCATTGGTAATACATGTGGGTCGTTTTGGACG
EST: gi|211405764|gb|FL399268.1|FL399268
EST:     GAAAGCTTTCATACTAAATATCGGAGGCATGAAAT-SGTGTCAGATTGAG                         TGGTGGTGAACCAGAAAAGCCATTGGTAATACATGTGGGTCGTTTTGGACG
genomic: GAAAGCTTTCATACTAAATATCGGAGGCATGAAATGCGTGTCAGATTGAGgtatcaccgc ... ctcccattagTGGTGGTGAACCAGAAAAGCCATTGGTAATACATGTGGGTCGTTTTGGACG
EST: gi|71300882|gb|DR786472.1|DR786472
EST:     GAAAGCTTTCATACTAAATATCGGAGGCATGAAATGCGTGTCAGATTGAG                         TGGTGGTGAACCAGAAAAGCCATTGGTTATACATGTGGGTCGTTTTGGA
genomic: GAAAGCTTTCATACTAAATATCGGAGGCATGAAATGCGTGTCAGATTGAGgtatcaccgc ... ctcccattagTGGTGGTGAACCAGAAAAGCCATTGGTAATACATGTGGGTCGTTTTGGA

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: 45 (upstream exon), 49 (downstream exon)
Score: 52

CAAACAGAATACGGCTTTGGAATAAGGGTGTAGATTCTGAAAGCTTTCATACTAAATATCGGAGGCATGAAATGCGTGTCAGATTGAGgtatcaccgc ... ctcccattagTGGTGGTGAACCAGAAAAGCCATTGGTAATACATGTGGGTCGTTTTGGACGTGAAAAAAATTTGGATTTTCTGAAAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 42

CAAACAGAATACGGCTTTGGAATAAGGGTGTAGATTCTGAAAGCTTTCATACTAAATATCGGAGGCATGAAATGCGTGTCAGATTGAGgtatcaccgc ... ctcccattagTGGTGGTGAACCAGAAAAGCCATTGGTAATACATGTGGGTCGTTTTGGACGTGAAAAAAATTTGGATTTTCTGAAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 47

CAAACAGAATACGGCTTTGGAATAAGGGTGTAGATTCTGAAAGCTTTCATACTAAATATCGGAGGCATGAAATGCGTGTCAGATTGAGgtatcaccgc ... ctcccattagTGGTGGTGAACCAGAAAAGCCATTGGTAATACATGTGGGTCGTTTTGGACGTGAAAAAAATTTGGATTTTCTGAAAAG


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 10

CAAACAGAATACGGCTTTGGAATAAGGGTGTAGATTCTGAAAGCTTTCATACTAAATATCGGAGGCATGAAATGCGTGTCAGATTGAGgtatcaccgc ... ctcccattagTGGTGGTGAACCAGAAAAGCCATTGGTAATACATGTGGGTCGTTTTGGACGTGAAAAAAATTTGGATTTTCTGAAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaggagtgttaagaaactttgaatggactaacaatttttttcctctcccattagTGGTGGTGAACCAGAAAAGCCATTGGTAATACATGTGGGTCGTTTTGGACGTGAAAAAAATTTGGATTTTCTGAAAAG
                          gactaac  putative branch site (score: 10)
                                caatttttttcctctc  CT-rich tract
                           actaacaattttttt  TA-rich tract