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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagccttatggcttgttgctaagtagtacttattgtggcatgcttcaagcatctatttgttttcccttctcttatcaccaagacaagaaaattattttttctgtaaatatagGTCTTCCTTGGCCAAAGCGGAGGCCTTGACTGTGAGGGAAATGAACTGCCACGATTGGTTTATGTTTCTAGAGAGAAACGACCAGGCTATAACCATCATA

Basic information

species Zea mays
transcript GRMZM2G025231_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025231_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os07g24190.1 (Oryza sativa), 3'ss of exon 8
gtaagcctta-tggcttgt--tgctaagtagtacttattgtggcatgcttcaagcatctatttgttttcccttctcttatcaccaagacaagaaaattatt-ttttctgtaaatatagGTCTTCCTTGGCCAAAGCGGAGGCCTTGACTGTGAGGGAAATGAACTGCCACGATTGGTTTATGTTTCTAGAGAGAAACGACCAGGCTATAACCATCATA
||| |      ||  ||||  || |    ||||  |||  ||||||  || | | |||   |  ||| |  ||||   || |  | || ||  || |||    |||||  |   ||||||||||||||||||||| || |||| ||||   || || ||||| || || |||||||| |||||||| ||||| ||| | ||||||||||||||||| |
gtatgttcgggtgatttgtgatggtgcacagtatatatgctggcat-tttgatggatcccctc-tttcctattcttgaattatgatgataaagaagttaaaactttctcaatgaatagGTCTTCCTTGGCCAAAGTGGCGGCCATGACATCGAAGGTAATGAGCTACCTCGATTGGTGTATGTTTCAAGAGAAAAAAGGCCAGGCTATAACCATCACA
















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|211308258|gb|FL341177.1|FL341177
EST:     GAACCCCCTGGCCTGGAAACAATGTTCGTGATCATCCTGGAATGATTCAG                         GTCTTCCTTGGCCAAAGCGGAGGCCTTGACTGTGAGGGAAATGAACTGCCA
genomic: GAACCCCCTGGCCTGGAAACAATGTTCGTGATCATCCTGGAATGATTCAGgtaagcctta ... gtaaatatagGTCTTCCTTGGCCAAAGCGGAGGCCTTGACTGTGAGGGAAATGAACTGCCA




















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), 45 (downstream exon)
Score: 125

AGTTGCCAAAGCCCAGAAAGTTCCTGAAGAAGGATGGACAATGCAAGATGGAACCCCCTGGCCTGGAAACAATGTTCGTGATCATCCTGGAATGATTCAGgtaagcctta ... gtaaatatagGTCTTCCTTGGCCAAAGCGGAGGCCTTGACTGTGAGGGAAATGAACTGCCACGATTGGTTTATGTTTCTAGAGAGAAACGACCAGGCTATAACCATCATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 351

AGTTGCCAAAGCCCAGAAAGTTCCTGAAGAAGGATGGACAATGCAAGATGGAACCCCCTGGCCTGGAAACAATGTTCGTGATCATCCTGGAATGATTCAGgtaagcctta ... gtaaatatagGTCTTCCTTGGCCAAAGCGGAGGCCTTGACTGTGAGGGAAATGAACTGCCACGATTGGTTTATGTTTCTAGAGAGAAACGACCAGGCTATAACCATCATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 173

AGTTGCCAAAGCCCAGAAAGTTCCTGAAGAAGGATGGACAATGCAAGATGGAACCCCCTGGCCTGGAAACAATGTTCGTGATCATCCTGGAATGATTCAGgtaagcctta ... gtaaatatagGTCTTCCTTGGCCAAAGCGGAGGCCTTGACTGTGAGGGAAATGAACTGCCACGATTGGTTTATGTTTCTAGAGAGAAACGACCAGGCTATAACCATCATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1237

AGTTGCCAAAGCCCAGAAAGTTCCTGAAGAAGGATGGACAATGCAAGATGGAACCCCCTGGCCTGGAAACAATGTTCGTGATCATCCTGGAATGATTCAGgtaagcctta ... gtaaatatagGTCTTCCTTGGCCAAAGCGGAGGCCTTGACTGTGAGGGAAATGAACTGCCACGATTGGTTTATGTTTCTAGAGAGAAACGACCAGGCTATAACCATCATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttcccttctcttatcaccaagacaagaaaattattttttctgtaaatatagGTCTTCCTTGGCCAAAGCGGAGGCCTTGACTGTGAGGGAAATGAACTGCCACGATTGGTTTATGTTTCTAGAGAGAAACGACCAGGCTATAACCATCATA
                                     ttttttctgt  CT-rich tract
                         acaagaaaattatttt  TA-rich tract