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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGGGCAACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaaaaaatgactgtcttatttgcctttgtacataccatgacattggactataacaatcagagcaatatagtgaaatcccttttcttgattttggttgaaatatgtttttcag

Basic information

species Zea mays
transcript GRMZM5G829738_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G829738_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os02g27950.2 (Oryza sativa), 5'ss of exon 14
TATGGGCAACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaaaaaatgactgtcttatttgcctttgtacataccatgacattggactataacaatcagagcaatatagtgaaatcccttttcttgattttggttgaaatatgtttttcag
|||||||| || |||| |||   ||||||||||||||| |||||||||||||| ||||||||  ||                | |  || | ||   | ||   | ||| ||  |||    |   |        | | || | || |  |  ||||     |              
TATGGGCAGCAGATGATGAT---GGGGCAGACTCGTCCTGTTTATTATTATGCACCTgtaagccaa----------------tgtatctgtataatcatcaaagctttgtacc-taatgccccctgtttctgtttaacattctttcttcttctttttccccag-------------

upper sequence: GRMZM5G829738_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os02g27950.1 (Oryza sativa), 5'ss of exon 14
------TATGGGCAACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaaaaaatgactgtcttatttgcctttgtacataccatgacattggactataacaatcagagcaatatagtgaaatcccttttcttgattttggttgaaatatgtttttcag
      |||||||| || |||| |||   ||||||||||||||| |||||||||||||| ||||||||  ||                | |  || | ||   | ||   | ||| ||  |||    |   |        | | || | || |  |  ||||     |              
TTGCAGTATGGGCAGCAGATGATGAT---GGGGCAGACTCGTCCTGTTTATTATTATGCACCTgtaagccaa----------------tgtatctgtataatcatcaaagctttgtacc-taatgccccctgtttctgtttaacattctttcttcttctttttccccag-------------
















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|31363999|gb|CD448354.1|CD448354
EST:     AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCT                         GAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
genomic: AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
EST: gi|116815752|gb|EC858445.1|EC858445
EST:     AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCT                         GAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
genomic: AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
EST: gi|28931133|gb|CB334494.1|CB334494
EST:     AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCT                         GAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
genomic: AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
EST: gi|83279263|gb|DV943271.1|DV943271
EST:     AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCT                         GAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTTTGAACTG
genomic: AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
EST: gi|6012574|gb|AW062011.1|AW062011
EST:     AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCT                         GAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTTTGAACTG
genomic: AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
EST: gi|60344962|gb|DN211935.1|DN211935
EST:     AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCT                         GAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
genomic: AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
EST: gi|60344398|gb|DN211371.1|DN211371
EST:     AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCT                         GAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
genomic: AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
EST: gi|116826672|gb|EC870479.1|EC870479
EST:     AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCT                         GAGATGCAACAATACAGAAGAAGAAACTTTTAGATATACCATTCTGAACTG
genomic: AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
EST: gi|74234144|gb|DT642058.1|DT642058
EST:     AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCT                         GAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
genomic: AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
EST: gi|78125642|gb|DV544026.1|DV544026
EST:     AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCT                         GAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
genomic: AACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
EST: gi|33097976|gb|CF057936.1|CF057936
EST:     TGACGATTGGGGGGCAGACTCGTCCTGTTTATTATTATGCGCCT                         GAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG
genomic: TGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTG

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: 144

TATGGGCAACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTGCTCTTAGATGGAAGTCGCTGCAATCCCCACAAGTGGGATTTTGACCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

TATGGGCAACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTGCTCTTAGATGGAAGTCGCTGCAATCCCCACAAGTGGGATTTTGACCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 108

TATGGGCAACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTGCTCTTAGATGGAAGTCGCTGCAATCCCCACAAGTGGGATTTTGACCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 74

TATGGGCAACAAATGACGATTGGGGGGCAGACTCGTCCAGTTTATTATTATGCGCCTgtaagttaaa ... tgtttttcagGAGATGCAACAATACAGAGGAAGAAACTTTTAGATATACCATTCTGAACTGCTCTTAGATGGAAGTCGCTGCAATCCCCACAAGTGGGATTTTGACCAGC