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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTGAATCTTGTGTATTCTCTGACGGTTGCTATACAAAGGACCTGACAATTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccctttccaatatgtaaaaactattctgatggacgcatttcccttgtcacttttatcttgatctctggtaagtctagtactctagtctagcac...

Basic information

species Zea mays
transcript GRMZM2G162347_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162347_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g43870.1 (Oryza sativa), 5'ss of exon 6
TCGTGAATCTTGTGTATTCTCTGACGGTTGCTATACAAAGGACCTGACAATTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgta-caatccctttccaatatgtaaaaactattctg-atggacgcatttcccttgtcacttttatcttgatctctggtaagtctagtactctagtctagcac
|||||| || ||| |||||||||| ||||||||||||||||| ||||||||||| ||  | ||| |||||||||||| ||||||||||||||||||||||||| ||  || ||| |   ||     |  |  | |  ||||||  ||     |  |  | ||| | | | |||    | || || |    ||||   |  | 
TCGTGAGTCATGTATATTCTCTGAGGGTTGCTATACAAAGGATCTGACAATTCTTGGAGTTGACCTGGCAAAAGTTGTAATAGTTGACAATACTCCACAGgtagcatgcctttttccgaatactgtatatgctttatatggacagatggaaatgtttccatttctatagttctagacttagacttggttgctaga--aatat
















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|32850497|gb|CD990178.1|CD990178
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGGTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|78179711|gb|DV550084.1|DV550084
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|211029103|gb|FL471471.1|FL471471
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|32832801|gb|CD972479.1|CD972479
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|6993978|gb|AW453192.1|AW453192
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|71533678|gb|DR784437.1|DR784437
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|116825971|gb|EC869721.1|EC869721
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGGAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTATGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|32833646|gb|CD973324.1|CD973324
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|32832678|gb|CD972356.1|CD972356
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|6865263|gb|AW360613.1|AW360613
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGCCAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|78074154|gb|DV502588.1|DV502588
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|32831928|gb|CD971606.1|CD971606
EST:     GATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCCCAG                         GTTTTCCAGTTGCAAGTGGATACCGGCATACCGATTAAGAGCTGGTTTGAT
genomic: GATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|78108659|gb|DV527077.1|DV527077
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|32835189|gb|CD974867.1|CD974867
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|32835374|gb|CD975052.1|CD975052
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|32835136|gb|CD974814.1|CD974814
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCATGTGGATAACGGCATACCGATTAAGAGCTGGNTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
EST: gi|211362627|gb|FL463911.1|FL463911
EST:     TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAG                         GTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT
genomic: TTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGAT

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: 83

TCGTGAATCTTGTGTATTCTCTGACGGTTGCTATACAAAGGACCTGACAATTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGATGACCCCTCAGATCAGGAACTGATCGAGTTGCTCCCGTTCTTGGAGAGCC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 159

TCGTGAATCTTGTGTATTCTCTGACGGTTGCTATACAAAGGACCTGACAATTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGATGACCCCTCAGATCAGGAACTGATCGAGTTGCTCCCGTTCTTGGAGAGCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 257

TCGTGAATCTTGTGTATTCTCTGACGGTTGCTATACAAAGGACCTGACAATTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGATGACCCCTCAGATCAGGAACTGATCGAGTTGCTCCCGTTCTTGGAGAGCC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 102

TCGTGAATCTTGTGTATTCTCTGACGGTTGCTATACAAAGGACCTGACAATTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccc ... ctttatctagGTTTTCCAGTTGCAAGTGGATAACGGCATACCGATTAAGAGCTGGTTTGATGACCCCTCAGATCAGGAACTGATCGAGTTGCTCCCGTTCTTGGAGAGCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTGAATCTTGTGTATTCTCTGACGGTTGCTATACAAAGGACCTGACAATTCTGGGGATCGACTTGGCAAAAGTTGCAATAGTTGACAATACTCCACAGgtacaatccctttccaatatgtaaaaactattctgatggacgcatttcccttgtcacttttatcttgatctctggtaagtctagtactctagtctagcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaacta