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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactcggcacttgctcaatcactgtgtttatgattaatttatctgactaacaagtaccaacaacctacag

Basic information

species Zea mays
transcript GRMZM2G047093_T01
intron # 22
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047093_T01 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os01g43030.1 (Oryza sativa), 5'ss of exon 22
ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactcggcacttgctcaatcactgtgt-ttatgattaatttatctgactaacaagtaccaacaacctacag
|||| ||| |||||||||||||||| ||||||    || | ||| |||||||| |||||||||||||||||| |||||||||| || || ||  | |||||  ||   ||   ||||     || | ||   |    |   ||||| |||||  |||||     ||        
ATAAGGTTTTTCCACAAGATAAACAATCTTCCCTCTCCAGGGACAGATTCTGAAAAGCTAATTTGGAATGTTTTGGAAGCTGAGCGTCCAGATTTAAGgtt--aagctggtttttgcattgccaatatgcacttctttcggtttatttgacttgcaagttattgcag-------
















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|20300007|gb|BQ162950.1|BQ162950
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagG-CAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAA
EST: gi|7227463|gb|AW566104.1|AW566104
EST:     GAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: GAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|32924622|gb|CF029434.1|CF029434
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|32924627|gb|CF029439.1|CF029439
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|19436527|gb|BM952937.1|BM952937
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGGTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|32923660|gb|CF028472.1|CF028472
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|32944990|gb|CF049809.1|CF049809
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|60345123|gb|DN212096.1|DN212096
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|211089342|gb|FL470619.1|FL470619
EST:     TCTGAGAAGTTAATTT-GAATGTTCT-GTAGCTGAAGGGCCTGACATGAG                         GCAATTACATGGAAAGTCCCTCG-TGGAGTAAACAG-AGTTTTCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|32924181|gb|CF028993.1|CF028993
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|32924574|gb|CF029386.1|CF029386
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|32924629|gb|CF029441.1|CF029441
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|211406573|gb|FL434917.1|FL434917
EST:     CTGAGAAGAT-ATATTGG-ATGATCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: CTGAGAAGCTAAT-TTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|32923887|gb|CF028699.1|CF028699
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|32923761|gb|CF028573.1|CF028573
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|60398052|gb|DN230868.1|DN230868
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|60340635|gb|DN207608.1|DN207608
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|31355959|gb|CD440316.1|CD440316
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|67014809|gb|CO443558.1|CO443558
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|33093540|gb|CF053534.1|CF053534
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|211430406|gb|FL005437.1|FL005437
EST:     TTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|60349287|gb|DN216260.1|DN216260
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|32934431|gb|CF039243.1|CF039243
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
EST: gi|32923755|gb|CF028567.1|CF028567
EST:     TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAG                         GCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA
genomic: TCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAA

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: 214

ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAAACACAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 232

ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAAACACAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 246

ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAAACACAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactc ... caacctacagGCAATTACATGGAAAGTCCCTCGTTGAAGTAAACAGAAGTTTCCTTGAAAAACACAATG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAAAGTTCTTCCACAAGATAAACAGTCTTCCTGGACCTGTGACTGATTCTGAGAAGCTAATTTGGAATGTTCTGGAAGCTGAACGACCTGACATGAGgttctaactcggcacttgctcaatcactgtgtttatgattaatttatctgactaacaagtaccaacaacctacag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA