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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcttttttgtgttttctttcttcgctcgtgttcttctccctcccctgtttgcctattgggaagtttcgtttcatggcgatgaatggtcgtcatggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGGTGCTCGACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATAC

Basic information

species Zea mays
transcript GRMZM2G126900_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126900_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os06g36560.1 (Oryza sativa), 3'ss of exon 1
gtgagcttttttgtgttttctttcttcgctcgtgttcttctccctcccctgtttgcctattgggaagtttcgt----ttcatggc--gatgaatgg-tcgt---------------------------catggc------gcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTG---------ACCCCGCGGAGCTGGTGCTCGACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATAC
|||||||  |     |||||| |||   ||| || | |  |   |||  |   ||   |     | |||  |     ||| |||   |||| |||| ||||                           |||||       ||||||||  | || ||  |||| ||| ||||||| || |         || | |||||||| |||||||||| ||||||||||||||||||| ||||||||||         
gtgagctcatgatccttttctctctct-ctcttgatttcttgattccagtccgtgaggaagaaaaggttcagcaatgttcctggatggatggatggatcgtggaactaattaaggttctaagttctgacatggttcgcttgcagATGCTATCGCCGACCGGAAGGTCGCCGGCGGCGGCGGCGGCGACAACGCGGCGGAGCTCGTGCTCGACGGCGGCTTCGTCGTGCCGGACTCCAACGCCTT---------
















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|148942392|gb|EC887411.2|EC887411
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211533476|gb|FL294724.1|FL294724
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211530464|gb|FL294704.1|FL294704
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211530470|gb|FL294710.1|FL294710
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGAAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAS-TGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|37424596|gb|CF650031.1|CF650031
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|78086722|gb|DV515115.1|DV515115
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211530473|gb|FL294713.1|FL294713
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGASSTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211533475|gb|FL294723.1|FL294723
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGASCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|148939596|gb|EC884223.2|EC884223
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211533468|gb|FL294716.1|FL294716
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211414693|gb|FL109921.1|FL109921
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTMCCCGGCGGAGGCGACCCCGCGGA-CTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211530472|gb|FL294712.1|FL294712
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|20300192|gb|BQ163135.1|BQ163135
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211530465|gb|FL294705.1|FL294705
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGTAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGG-AAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTG
EST: gi|211530467|gb|FL294707.1|FL294707
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211533473|gb|FL294721.1|FL294721
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211530463|gb|FL294703.1|FL294703
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211533477|gb|FL294725.1|FL294725
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211533471|gb|FL294719.1|FL294719
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGA-CTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|15005365|gb|BI325432.1|BI325432
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211530466|gb|FL294706.1|FL294706
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|148962202|gb|EE013017.2|EE013017
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211530461|gb|FL294701.1|FL294701
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211530469|gb|FL294709.1|FL294709
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211530474|gb|FL294714.1|FL294714
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211533478|gb|FL294726.1|FL294726
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211533469|gb|FL294717.1|FL294717
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGAAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211533474|gb|FL294722.1|FL294722
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAS-TGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|211533470|gb|FL294718.1|FL294718
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGCGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
EST: gi|15177491|gb|BI398430.1|BI398430
EST:     GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCG                         ATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG
genomic: GCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGG

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: 36 (upstream exon), 34 (downstream exon)
Score: 7

CATTTTGCCAAGGCTAGCCCCCTCCTCCTCTTCTTCCTCTTCTTCTTTTCGCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGGTGCTCGACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 540

CATTTTGCCAAGGCTAGCCCCCTCCTCCTCTTCTTCCTCTTCTTCTTTTCGCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGGTGCTCGACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 204

CATTTTGCCAAGGCTAGCCCCCTCCTCCTCTTCTTCCTCTTCTTCTTTTCGCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGGTGCTCGACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 443

CATTTTGCCAAGGCTAGCCCCCTCCTCCTCTTCTTCCTCTTCTTCTTTTCGCGACGATCAGAGAAGAAGATGACGATCACCATTGAACAGCCCCAGCTCGgtgagctttt ... catggcgcagATGCGGTGGCGGAGAGGAAAGTCCCCGGCGGAGGTGACCCCGCGGAGCTGGTGCTCGACGCCGGCTTCGTCGTGCCGGACGCCAACGCCTTCGGCAATAC