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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atacatcacccaaccccaagttaggattagtgtttcccacagcgaggacaactaggcaatagcttgctcattgtataatgttgctccctacattctgcagGGATGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTTCGAGTG

Basic information

species Zea mays
transcript GRMZM2G153138_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153138_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 7
-atacatcacccaaccccaagttaggattagtgtttcccacagcgaggacaactaggcaatagcttgctcattgtataatgttgctccctacattctgcagGGATGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTTCGAGTG
   | | |   |||    |      |  | |  | |     | |      |||||   | |         ||  || |||  || |     |||| | ||||||||||||||||||||| || ||||| |||||||||||||| |||||  ||||||| |||||||| |||||||| || |||||||||||||||||||||
tgaaaagctggcaaaagtagcccttggctggcatctgtattatctcatttaactatttattgcaacatatatactaaaattctggtttggccatt-tacagGGATGAGGAACTTATGTCACAAGGGCTTGCACTGAATGATGACTTGCAACGTGTTCTCGCAAAACACGATGCAATTGCTGCAGGCATTGCAGTTCGAGTG
















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|71441431|gb|DR822481.1|DR822481
EST:     CAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCAC                         GGATGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAG
genomic: CAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgtgc ... cattctgcagGGATGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAG
EST: gi|78089227|gb|DV517601.1|DV517601
EST:     CAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCAC                         GGATGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAG
genomic: CAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgtgc ... cattctgcagGGATGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAG
EST: gi|87152145|gb|DY396934.1|DY396934
EST:     CAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCAC                         GGACGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAG
genomic: CAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgtgc ... cattctgcagGGATGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAG

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), 48 (downstream exon)
Score: 100

GGATTAAGGCAGGAGGTAATTGTGGAACTCGTGGACCAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgtgc ... cattctgcagGGATGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTTCGAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 242

GGATTAAGGCAGGAGGTAATTGTGGAACTCGTGGACCAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgtgc ... cattctgcagGGATGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTTCGAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

GGATTAAGGCAGGAGGTAATTGTGGAACTCGTGGACCAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgtgc ... cattctgcagGGATGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTTCGAGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 333

GGATTAAGGCAGGAGGTAATTGTGGAACTCGTGGACCAATGCCGCACTTACAAGCAGAGAGTAGTGCAGCTAGTTAATTCTACCACgtgagtgtgc ... cattctgcagGGATGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTTCGAGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggacaactaggcaatagcttgctcattgtataatgttgctccctacattctgcagGGATGAGGAACTTATGTCGCAGGGGCTCGCACTGAATGATGATTTGCAGAGTGTTCTAGCAAAACATGATGCAATAGCAGCAGGCATTGCAGTTCGAGTG
                                      ctccctac  CT-rich tract
                        attgtataat  TA-rich tract