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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgtttacgcttatatgctctttttgttatttatttagtttttttttgcttttcattttctatgtactaatgcaagtgttatcaactttttttttggcag

Basic information

species Zea mays
transcript GRMZM2G079196_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 5'ss of exon 9
GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgtttacgcttatatgctctttttgttatttatt-tagtttttttttgcttttcattttctatgtactaatgcaagtgttatcaact--ttttttttggcag-------
|||||| ||||||||||| ||||| || ||||||||| |||||||||| || |||||||||||||||||||||||||||||||| || |||||    |||   |   || |   | | ||| |||||  |  ||   || |  |||  | |||  || |  | | || |  |  || | |  |  || ||     ||        
GTACAAAAATGATCCTGAGATCCTCGCCATGACAAACTTGATTGCAGCATATCAGAAGAATGACATCATGGAATTTGAAAAGATTCTAAAGgtcagtgttattgaacat-tatccatcttgctattttctgcagcaattctaagctagttatt--ctgttaattgattctggatttctgatgtgattgttacaaacaaaattcag

upper sequence: GRMZM2G079196_T01 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA03G00670.1 (Glycine max), 5'ss of exon 9
GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgt--tgtcgtt--------tacgcttatatgctctttttg--ttatttatttagt-ttttttttgcttttcattttctatgtact--aatgcaagtgttatcaactttttttttggcag
 ||||||||||| ||||||||  | |||||||||||| |||| ||||| || |||  |||||| ||  |||||||||| || ||| |||||||  | |  ||         |||   |||||       |   ||    ||  | | ||| | ||  |||||||    ||| |  |  |||   |   ||   || ||  |||   |   
ATACAAGAATGACCCTGAAATTTTGGCAATGACAAACTTGATAGCAGCCTATCAGCGGAATGAAATATTGGAATTTGAGAAAATCTTGAAGgtacttttattgagtctagcacgagaatatgtctgcactaacttgaccataaaatatttctcttatttttcatccaatatttgttggaatttgatatttggtaagttactttccag---
















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|24768954|gb|CA404083.1|CA404083
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|33096883|gb|CF056843.1|CF056843
EST:     GTACCAGAAGAACGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: GTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|67012630|gb|CO441379.1|CO441379
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|211450030|gb|FL052872.1|FL052872
EST:     TTGCAGCGTACCAKAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|211507840|gb|FL110003.1|FL110003
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|67023333|gb|CO452082.1|CO452082
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|211507839|gb|FL110002.1|FL110002
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|74246199|gb|DT654113.1|DT654113
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|18659527|gb|BM500385.1|BM500385
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGA
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGA
EST: gi|83279086|gb|DV943094.1|DV943094
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|37375261|gb|CF624055.1|CF624055
EST:     CAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: CAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|211507835|gb|FL109998.1|FL109998
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|211450033|gb|FL052875.1|FL052875
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|45847141|gb|CN071084.1|CN071084
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|60394631|gb|DN227501.1|DN227501
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
EST: gi|211507838|gb|FL110001.1|FL110001
EST:     TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAG                         AGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG
genomic: TTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAG

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), 48 (downstream exon)
Score: 362

GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAGGACTTATTGAAGAACATCAGAACCCAAGTGCTGCTCAAGCTTATTAAAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 604

GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAGGACTTATTGAAGAACATCAGAACCCAAGTGCTGCTCAAGCTTATTAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 426

GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAGGACTTATTGAAGAACATCAGAACCCAAGTGCTGCTCAAGCTTATTAAAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 547

GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgttt ... tttttggcagAGTAATAGAAGAACAATAATGGACGATCCTTTTATCCGTAACTATATTGAGGACTTATTGAAGAACATCAGAACCCAAGTGCTGCTCAAGCTTATTAAAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACAAGAATGATCCTGAAATCCTTGCAATGACAAACCTGATTGCAGCGTACCAGAAGAATGACATCATGGAATTTGAAAAGATCCTGAAGgttgtcgtttacgcttatatgctctttttgttatttatttagtttttttttgcttttcattttctatgtactaatgcaagtgttatcaactttttttttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG