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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCTTCCCCGTCGACCAGGAGATCAACTCTAGGATCTATCTCTGGCGTGGCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattcccgtccccacctcgcatcagtgctgggaattggacaattttttttgtgctataagctcctgtctttgttccggggattcgtgcag

Basic information

species Zea mays
transcript GRMZM5G836588_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836588_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os10g30750.1 (Oryza sativa), 5'ss of exon 1
GCGCTTCCCCGTCGACCAGGAGATCAACTCTAGGATCTATCTCTGGCGTGGCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattcccgtccccacctcgcatcagtgctgggaattggacaattttttttgtgctataagctcctgtctttgttccggggattcgtgcag
| | |||||||||||||| ||||||||||| |||||||| |||||| | ||||| ||||||||||| ||||||||||| |||||||| || || ||||||||  ||||||  ||     | ||   | | |  |||  | |    |       ||||| ||       | ||   || |  |||||||| |||||
GAGGTTCCCCGTCGACCACGAGATCAACTCCAGGATCTACCTCTGGAGGGGCCACCCCTGGAACCTGGAGGTCGACGCTGTCGTCAACTCCACTAACGAGgttgcgattctagttttatcttcttgtgaattgtggagagttagaa-------ttgtggtactcagctcggt---tgctttggggattc-tgcag
















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|211381535|gb|FL250722.1|FL250722
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
EST: gi|76286118|gb|DV025686.1|DV025686
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
EST: gi|211381543|gb|FL250730.1|FL250730
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
EST: gi|211381540|gb|FL250727.1|FL250727
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
EST: gi|211381538|gb|FL250725.1|FL250725
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCA-AGTAAGCCCGGGGTTGCATGCTGCTGCCGGGTC
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTA-GCCCGGGGTTGCATGCTGCTGCCGGGTC
EST: gi|211378900|gb|FL250717.1|FL250717
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
EST: gi|211378897|gb|FL250714.1|FL250714
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
EST: gi|211378901|gb|FL250718.1|FL250718
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCACAGNTAGCCCGGGGTTGCATGCTGCTGCCCGGTC
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAG-TAGCCCGGGGTTGCATGCTGCTGCCGGGTC
EST: gi|91051901|gb|EB162319.1|EB162319
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
EST: gi|211381541|gb|FL250728.1|FL250728
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
EST: gi|148931777|gb|EC875053.2|EC875053
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
EST: gi|211378903|gb|FL250720.1|FL250720
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCACAGTAG
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAG
EST: gi|94478487|gb|EB707445.1|EB707445
EST:     GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAG                         AGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA
genomic: GCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCA

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), 48 (downstream exon)
Score: 44

GCGCTTCCCCGTCGACCAGGAGATCAACTCTAGGATCTATCTCTGGCGTGGCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 90

GCGCTTCCCCGTCGACCAGGAGATCAACTCTAGGATCTATCTCTGGCGTGGCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTG


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

GCGCTTCCCCGTCGACCAGGAGATCAACTCTAGGATCTATCTCTGGCGTGGCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 62

GCGCTTCCCCGTCGACCAGGAGATCAACTCTAGGATCTATCTCTGGCGTGGCCAGCCCTGGAACCTCGAGGTCGACGCGGTCGTCAATTCTACCAACGAGgtctcgattc ... attcgtgcagAGCTTGGACGAGGCGCACAGTAGCCCGGGGTTGCATGCTGCTGCCGGGTCAGGGCTCGCCGAGGAGTGCGCCACCTTG