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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTGGGGATAGGCGTAGGACCGTTATGAGGCCACCACAAGTTCTTAGGGAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttcaacataattgtggcagcatattttttactgatactccctcgcctccttaaattgtctctgctgcttcgttgataaaattacaaaaaaaaataacttttaatttgtatctccag

Basic information

species Zea mays
transcript GRMZM2G080048_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G080048_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g48300.1 (Oryza sativa), 5'ss of exon 7
TTGCTGGGGATAGGCGTAGGACCGTTATGAGGCCACCACAAGTTCTTAGGGAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttcaacataattgtggcagcatattttttactgatactccctcgcctccttaaattgtctctgctgcttcgttgataaaattacaaaaaaaaataacttttaatttgtatctccag
||||||| || || || || || || |||||||| ||||| |||||| | ||||| || ||||||||||||||||| || |||||||| ||||| |||||||  | ||   ||  |||  |   | || || | |  ||||| ||  | |  | ||   |   |   |   |||    |||| || | ||   |||  ||   |   |              
TTGCTGGAGACAGACGCAGAACTGTCATGAGGCCGCCACAGGTTCTTCGAGAGGGCACGAAGAAGACAGTTTTTGTGAATTTTATGGACTTGTGCAAAACgtgcgctttttcaccatttggattgtattttgtat-ttgatattctattgaatgctcttacaatggataaagctg---tgatgaactaaccggaaattat--ttaccag-------------
















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|71300898|gb|DR786478.1|DR786478
EST:     AGTTTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: AGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|60399446|gb|DN232258.1|DN232258
EST:     GGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: GGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|211375010|gb|FL430791.1|FL430791
EST:     GAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: GAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|60354326|gb|DN221299.1|DN221299
EST:     GAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: GAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|94473773|gb|EB702731.1|EB702731
EST:     GAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: GAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|32863955|gb|CF003637.1|CF003637
EST:     GGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: GGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|26455990|gb|CA827573.1|CA827573
EST:     GAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: GAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|6194479|gb|AW146583.1|AW146583
EST:     GAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: GAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|60357822|gb|DN224795.1|DN224795
EST:     TAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: TAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|19822348|gb|BQ048372.1|BQ048372
EST:     GAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: GAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|60395435|gb|DN228305.1|DN228305
EST:     AGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: AGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|32863956|gb|CF003638.1|CF003638
EST:     GGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: GGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|14191391|gb|BG833621.1|BG833621
EST:     GGGAACAAAGAAGACAGTGTTGTTGTTAATTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: GGGAACAAAGAAGACAGT-TT-TTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|211047495|gb|FL474402.1|FL474402
EST:     TTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGG
genomic: TTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCAT-AGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGG
EST: gi|60347700|gb|DN214673.1|DN214673
EST:     TTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: TTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
EST: gi|60398984|gb|DN231800.1|DN231800
EST:     GAGGG-ACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAAC                         GATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG
genomic: GAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGG

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: 337

TTGCTGGGGATAGGCGTAGGACCGTTATGAGGCCACCACAAGTTCTTAGGGAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGGAACAAGCGGGTCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 322

TTGCTGGGGATAGGCGTAGGACCGTTATGAGGCCACCACAAGTTCTTAGGGAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGGAACAAGCGGGTCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 278

TTGCTGGGGATAGGCGTAGGACCGTTATGAGGCCACCACAAGTTCTTAGGGAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGGAACAAGCGGGTCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 462

TTGCTGGGGATAGGCGTAGGACCGTTATGAGGCCACCACAAGTTCTTAGGGAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttca ... gtatctccagGATGCATAGGCAACCTGAGCATGTGATGATGTTTTTACTTGCTGAAATGGGAACAAGCGGGTCACTTGATGGGCAGCAAAGGTTGGTGATCAAAGGAAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTGGGGATAGGCGTAGGACCGTTATGAGGCCACCACAAGTTCTTAGGGAGGGAACAAAGAAGACAGTTTTTGTTAACTTTATGGATTTGTGTAAAACgtaagtttcaacataattgtggcagcatattttttactgatactccctcgcctccttaaattgtctctgctgcttcgttgataaaattacaaaaaaaaataacttttaatttgtatctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG