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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcttttatctggaaaatccactgctccttagcctaaactgtatcttcagtgtgcatgataaatattacctgttttttttacagTTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCCTGGGGATCCTCCCTTTTCCCCACCGCCTCCATTCAATCCTCCGTCTCCT

Basic information

species Zea mays
transcript GRMZM2G150024_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150024_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv07s0031g01410.t01 (Vitis vinifera), 3'ss of exon 6
gtcttttatc--tggaaaatccactgct-ccttagcctaaactgtatcttcagtgtgcatgataaatattacctgttttt--tttacagTTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCCTGGGGATCCTCCCTTTTCCCCACCGCCTCCATTCAATCCTCCGTCTCCT
|| || |     ||     |  |   ||  | | |  |  | ||  |  |      |  | ||    |||     |||    | | |||||||   |||||    ||||| ||||| || |||| |  ||||||||||||||||  |||||| ||||| ||||| ||||||||    || || ||| | 
gttttatgctgatgcttgttgtaaaactgtcatggttttgaatgcctggtataaaagtgttatgctaattggtgatttaccatctgcagTTTTGCAAATAACTTGAATCTATGTGGTCCGGTTATTGGGAAGCCCTGCCCTGGGTCTCCTCCATTTTCTCCACCACCTCCATTTGTGCCACCATCTACA
















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|26456609|gb|CA828192.1|CA828192
EST:     TCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAG                         TTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCC
genomic: TCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAGgtcttttatc ... ttttttacagTTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCC
EST: gi|22542236|gb|BU092674.1|BU092674
EST:     TCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAG                         TTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCC
genomic: TCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAGgtcttttatc ... ttttttacagTTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCC
EST: gi|26559220|gb|CA831455.1|CA831455
EST:     TCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAG                         CTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGCAGCCCTGCCC
genomic: TCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAGgtcttttatc ... ttttttacagTTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCC
EST: gi|20512844|gb|BQ280038.1|BQ280038
EST:     TCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAG                         TTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCC
genomic: TCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAGgtcttttatc ... ttttttacagTTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCC
EST: gi|87156676|gb|DY401465.1|DY401465
EST:     TCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAG                         TTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCC
genomic: TCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAGgtcttttatc ... ttttttacagTTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCC

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: 48 (upstream exon), 46 (downstream exon)
Score: 68

GGATCTCTCGAGTAACAACCTCTCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAGgtcttttatc ... ttttttacagTTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCCTGGGGATCCTCCCTTTTCCCCACCGCCTCCATTCAATCCTCCGTCTCCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 83

GGATCTCTCGAGTAACAACCTCTCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAGgtcttttatc ... ttttttacagTTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCCTGGGGATCCTCCCTTTTCCCCACCGCCTCCATTCAATCCTCCGTCTCCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 99

GGATCTCTCGAGTAACAACCTCTCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAGgtcttttatc ... ttttttacagTTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCCTGGGGATCCTCCCTTTTCCCCACCGCCTCCATTCAATCCTCCGTCTCCT


Block sizes: 32 (upstream exon), 48 (downstream exon)
Score: 25

GGATCTCTCGAGTAACAACCTCTCAGGACCAGTCTCATCCAATGGCTCCTTTTCACTCTTCACCCCTATAAGgtcttttatc ... ttttttacagTTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCCTGGGGATCCTCCCTTTTCCCCACCGCCTCCATTCAATCCTCCGTCTCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagcctaaactgtatcttcagtgtgcatgataaatattacctgttttttttacagTTTTAACAATAATCCAAATCTTTGTGGCCCTGTTACTACGAAGCCCTGCCCTGGGGATCCTCCCTTTTCCCCACCGCCTCCATTCAATCCTCCGTCTCCT
  gcctaaa  putative branch site (score: 25)
                                    ttacctgtttttttt  putative PPT
                             ataaatattacctgtt  TA-rich tract