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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatattaggttcaatgtgtgcccttctgcagtacttagttttctttcatgctaatgactatttgaaatgaaaatttcctatag

Basic information

species Zea mays
transcript GRMZM5G833124_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 5'ss of exon 4
GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgca-tatattaggttcaatgtgtgcccttctgcagtacttagttttctttcatgctaatgactatttgaaatgaaaatttcctatag
||||| ||||| || |||||||| |||||||||||||||||||||||||||||||| || ||||| ||||||||||| ||| |    | ||   | |||  || |   |  |||  ||||  |  |||| ||  |||  | ||||   |  ||  ||  ||
GATGGAGCTGGCCGAGTTGGAAAAATGCTTTTTGCCCGCCAAGGGAAGAAATTTGACTACGACCTAAAGCAGgtgcaatatttggaatccatgttttgcaattattttgagctttattttgctctatgcaaaaaactgatcgaaa-acactttcacttcag

upper sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT5G49820.1 (Arabidopsis thaliana), 5'ss of exon 4
GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatattag-gttcaatgtgtgcccttctgcagtacttagttttctttcatgctaatgactatttgaaatgaaaatttcctatag
||||| |||||||||||||| || |||||||||||  | || || |||||||||||||||||  |||| ||||| | |||   |    | ||    |||  |  |  | |   |   |  | || |  || |       ||| |                 
GATGGTGCTGGGCGTGTTGGGAAAATGCTTTTTGCGAGGCAGGGAAAGAAATTTGATTATGATTTGAAACAGgtacttattccattacttaacaaatgcgatggttgactctctctctcacgtttaaactcactttggcttgcag----------------

upper sequence: GRMZM5G833124_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 5'ss of exon 4
GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatata--ttaggt-----tcaatgt----gtgcccttctgcagtacttagttttctttcatgctaatgactatttgaaatgaaaatttcctatag
||||| ||||| |||||||| || ||||||||||| || ||||||||||| ||||||||||| || || |||||  |  ||   || |      |  || |    ||   ||| | | | ||| | ||  | |  ||  |      | ||  || |    || |  |  ||
GATGGTGCTGGTCGTGTTGGGAAAATGCTTTTTGCACGGCAAGGGAAGAAGTTTGATTATGATCTAAAACAGgtaaaattagtctaagcactagttgattttgaagtcaacttttactggactgaattaacatatattattcattttcttaaaatttgtgatgtgtttcag

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|211214593|gb|FL385234.1|FL385234
EST:     GATGCTTTTTGCCCNGCCAGGGGAAGAAATTTGATTATGACCTGAAGCAG                         CTACCCTTTTTCTGGTGATCTCCTTGATGAATTTAGGACCTGGGGATAGAA
genomic: GATGCTTTTTGCCC-GCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTT-CTGGTGATCTC-TTGATGGAGTTAGGAGCTGGG-ATAGAA
EST: gi|19822663|gb|BQ048687.1|BQ048687
EST:     AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG                         CTACGCTTTTCTGGTGATCTCTTGATGGAATTAGGAGCTGGGATAGAATTA
genomic: AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTA
EST: gi|32931635|gb|CF036447.1|CF036447
EST:     AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG                         CTACGCTTTTCTGGTGATCTCTTGATGGAATTAGGAGCTGGGATAGAATTA
genomic: AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTA
EST: gi|18450494|gb|BM428772.1|BM428772
EST:     AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG                         CTACGCTTTTCTGGTGATCTCTTGATGGAATTAGGAGCTGGGATAGAATTA
genomic: AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTA
EST: gi|60356183|gb|DN223156.1|DN223156
EST:     TGACCTGAAGCAG                         CTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTA
genomic: TGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTA
EST: gi|91876063|gb|EB406020.1|EB406020
EST:     AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG                         CTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGG
genomic: AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGG
EST: gi|19822664|gb|BQ048688.1|BQ048688
EST:     AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG                         CTACGCTTTTCTGGT
genomic: AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGT
EST: gi|87153939|gb|DY398728.1|DY398728
EST:     AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG                         CTACGCTTTTCTGGTGATCTCTTGATGGAATTAGGAGCTGGGATAGAATTA
genomic: AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTA
EST: gi|71440154|gb|DR821204.1|DR821204
EST:     AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG                         CTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAAATA
genomic: AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTA
EST: gi|18649305|gb|BM498124.1|BM498124
EST:     AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG                         CTACGCTTTTCTGGNGATCTCTTGATGGAATTAGGAGCTGGGATAGAATTA
genomic: AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTA
EST: gi|32932638|gb|CF037450.1|CF037450
EST:     AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG                         CTACGCTTTTCTGGTGATCTCTTGATGGAATTAGGAGCTGGGATAGAATTA
genomic: AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTA
EST: gi|93281685|gb|EB673949.1|EB673949
EST:     AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAG                         CTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTA
genomic: AGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTA

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: 63

GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTAGCTACTGCAGCTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 179

GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTAGCTACTGCAGCTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 199

GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTAGCTACTGCAGCTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 136

GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatat ... tttcctatagCTACGCTTTTCTGGTGATCTCTTGATGGAGTTAGGAGCTGGGATAGAATTAGCTACTGCAGCTTTCCCACAGCTTTTCCTACCAATGGCATGCATAGCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGGGCTGGGCGTGTTGGAAAGATGCTTTTTGCCCGCCAAGGGAAGAAATTTGATTATGACCTGAAGCAGgtgcatatattaggttcaatgtgtgcccttctgcagtacttagttttctttcatgctaatgactatttgaaatgaaaatttcctatag

- - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC