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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaatagcatcctgtcccgatacttttttgtgagatttgtcaaatactcctacgtaaatagaagtagaaatcatttttttcatttaagtcttctaatacctgatataatttattttgctactgatttccatgtag

Basic information

species Zea mays
transcript GRMZM2G314386_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G314386_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g49530.1 (Oryza sativa), 5'ss of exon 2
AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaatagcatcctgtcccgatacttttttgtgagatttgtcaaatactcctacgtaaatagaagtagaaatcatttttttcatttaagtcttctaatacctgatataatttattttgctactgatttccatgtag
   | |||| ||| |||||||| |||   |||||||| ||||| |||||||| |||||||||||||| |  | |      |    || ||  |||   || |||   ||||||         | |||||||||   |||  |||| |  || | ||| | |||||| |    || | |||||||| |||||   ||  ||
GACTGCTTGCAGCTGAAATACCGGACACACATGACTTGTCATCAGGTGTGCTGTGTCAGGGgtatgtgactgtactagcgcagtttatttccttgaatgagttgc--aatactt--------agagaagtagaggacataattttgagcta-gccttttgatacctaactggatctcttttgctattgattgttatccag
















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|211133492|gb|FL236781.1|FL236781
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|71442944|gb|DR823994.1|DR823994
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|149044645|gb|EE047617.2|EE047617
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|32837769|gb|CD977447.1|CD977447
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGG
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|148970703|gb|EE021421.2|EE021421
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|211311913|gb|FL092761.1|FL092761
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTCTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|74239171|gb|DT647085.1|DT647085
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|71449060|gb|DR830110.1|DR830110
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|211311911|gb|FL092759.1|FL092759
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|148965413|gb|EE016213.2|EE016213
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|148933697|gb|EC877601.2|EC877601
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|211311912|gb|FL092760.1|FL092760
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|149073230|gb|EE161514.2|EE161514
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|32838159|gb|CD977837.1|CD977837
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|71442943|gb|DR823993.1|DR823993
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|211311910|gb|FL092758.1|FL092758
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGTG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
EST: gi|71775328|gb|DR973206.1|DR973206
EST:     GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGG                         GTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC
genomic: GCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGC

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), 47 (downstream exon)
Score: 88

AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGCAAATCTTGGTGAAGAATTTTCTCTTGATTCCCTCCCTCATTTAGACCGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGCAAATCTTGGTGAAGAATTTTCTCTTGATTCCCTCCCTCATTTAGACCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 124

AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGCAAATCTTGGTGAAGAATTTTCTCTTGATTCCCTCCCTCATTTAGACCGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 31

AGTTTCTTGGAGCAGAAATACCTGACGTGCATGACTTATCATCCGGTGTGCTTTGTCAGGGgtatgtaata ... ttccatgtagGTGGACAATTGAAACAAAGTATTATTCAGCTGATCTTTCCATCTGGACAGCAAATCTTGGTGAAGAATTTTCTCTTGATTCCCTCCCTCATTTAGACCGG