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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttagacaaggcttattatttgagattgctatttgtgccatgtaattttcattttatagcaccagcacattttttattttacattaccagaatgttattttttgtattctctgtgaattctttgtgcctacgacagcatatattcattaatactgatcatatagtgcaattgctacag

Basic information

species Zea mays
transcript GRMZM2G042027_T05
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042027_T05 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g29860.3 (Oryza sativa), 5'ss of exon 4
---------GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttagacaaggcttattatttgagattgctatttg--tgc-catgtaattttcattttatagcaccagcacattttttattttacattaccagaatgttattttttgtattctctgtgaattctttgtgcctacgacagcatatattcattaatactgatcatatagtgcaattgctacag
         ||| |||||  ||||||| ||  | || || || || ||||||||| ||||||| ||  ||||||||||| ||||||| ||||||||||||||||||||        |||  || |       ||| |||  ||| | |  ||| || ||      | || | |    | ||||||||  || | |    |||| |                                                                                
TGCTTGTAGGGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACTGGAGACTTTTCCTGAAAATTTGAGTGCTGTTGCCCATTTTgtaagttaacatgcatttaacatgtttttgcactagttgattgcacgtagaatgttgatcaggctgtac-atcgtgctgtttattttgtataatc----tgtttt--------------------------------------------------------------------------------

upper sequence: GRMZM2G042027_T05 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g29860.1 (Oryza sativa), 5'ss of exon 5
GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttagacaaggcttattatttgagattgctatttg--tgc-catgtaattttcattttatagcaccagcacattttttattttacattaccagaatgttattttttgtattctctgtgaattctttgtgcctacgacagcatatattcattaatactgatcatatagtgcaattgctacag
||| |||||  ||||||| ||  | || || || || ||||||||| ||||||| ||  ||||||||||| ||||||| ||||||||||||||||||||        |||  || |       ||| |||  ||| | |  ||| || ||      | || | |    | ||||||||  || | |    |||| |                                                                                
GGCTTCTGCTGTATTTGTGGGAATATACGAACCGACAAAAAGAAAACTACTGGAGACTTTTCCTGAAAATTTGAGTGCTGTTGCCCATTTTgtaagttaacatgcatttaacatgtttttgcactagttgattgcacgtagaatgttgatcaggctgtac-atcgtgctgtttattttgtataatc----tgtttt--------------------------------------------------------------------------------
















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|211371111|gb|FL037583.1|FL037583
EST:     GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT                         ACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
genomic: GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
EST: gi|71436673|gb|DR817723.1|DR817723
EST:     GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT                         ACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
genomic: GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
EST: gi|71302083|gb|DR787129.1|DR787129
EST:     GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT                         ACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
genomic: GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
EST: gi|76011416|gb|DT938586.1|DT938586
EST:     AAATCTGAGTGCAG-TGCCCCATTTT                         ACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTAC
genomic: AAATCTGAGTGCAGTTG-CCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTAC
EST: gi|50325364|gb|CO520490.1|CO520490
EST:     GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT                         ACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
genomic: GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
EST: gi|60342707|gb|DN209680.1|DN209680
EST:     GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT                         ACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
genomic: GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
EST: gi|91054196|gb|EB164614.1|EB164614
EST:     GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT                         ACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
genomic: GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
EST: gi|67018887|gb|CO447636.1|CO447636
EST:     CCTTCCTTAAAATCTGAGTGCAGTTGCCCATTTT                         ACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
genomic: CCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
EST: gi|78083391|gb|DV511784.1|DV511784
EST:     GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTT                         ACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA
genomic: GAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACA

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), 49 (downstream exon)
Score: 58

GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 103

GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 53

GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG


Block sizes: 47 (upstream exon), 44 (downstream exon)
Score: 46

GGCCTCTGCGATATTTGTCGGGGTGTATGAGCCAACTAAAAGAAAATTACTGGAAACCCTTCCTGAAAATCTGAGTGCAGTTGCCCATTTTgtaagttaga ... attgctacagACTGCAGGGGCCATTGGAGGTATTGCTGCTTCCCTCGTCCGTGTCCCTACAGAG