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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatactttattttggaatgtcctttactgccacattcattaaacctagcttcttctgtataagcctatttttagtgtgcttcacaaacagattattta...

Basic information

species Zea mays
transcript GRMZM2G058498_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os08g07960.2 (Oryza sativa), 5'ss of exon 7
ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaat---actttattttggaatgtccttta--ctgccacattcattaaacctagcttcttctgtataagcctatttttagtgtgcttcacaaacagattattta
|||||||||||||| |||||||| ||||| |||||||||||  |||| |||||||||||||| ||||||||||| |||||||||||   ||||| ||||| ||     | ||  ||     |     | ||        ||  | ||  |    ||| ||| ||| ||| |    |   || |   
ACGGAGTTCAAGCGCATCCAATCGCCACTCAAATACCAGACTAGGTGTCTTGCTGCATTCCCGGATCAACAAGGATTTTTGgtaatgcaacttttttttgtaaaaatttctagtctattctaaatgcttaaatagataactattctagcaatgcattgtta-tgtactt-atggtctttttct---

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA08G19260.1 (Glycine max), 5'ss of exon 6
ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatactttattttggaatgtcctttactgccacattcattaaacctagcttcttctgtataagcctatttttagtgtgcttcacaaacagattattta----
   || |||||| ||||    |||||| |||| || || ||| ||||||||||||||||||||||||||||||| || |||||| | | |  ||      | |  ||||       |   | |||    |  ||        |  |    | ||| || | ||  |   ||  ||| | |     
GTTGAATTCAAGAGAATTGTTTCACCATTAAAGTATCAAACAAGGTGCCTTGCTGCATTCCCTGATCAACAAGGTTTCTTGgta-tgcatctttcctatctttattttatcagtgaaa--agtaatatcatgtttccaacagtgggttcctattttgtat-ctagaaggacttattttctgtaac

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 7
lower sequence: GLYMA15G05740.1 (Glycine max), 5'ss of exon 6
ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatactttattttggaatgtcctttactgccacattcatt--aaacctagcttcttctgtataagcctatttttagtgtgcttcacaaacagattattta-
   || |||||| ||||    |||||  | || || || ||| |||||||||||||||||||||| |||||||| || ||||||    | | |         |     |    ||      ||    |  | | |  || | | |   || || |||| | |       |||   | || | | 
GTTGAATTCAAGAGAATTGTTTCACCCTTGAAGTATCAAACAAGGTGCCTTGCTGCATTCCCTGACCAACAAGGTTTCTTGgtatgcatctctccccactcctttaagatcttcaatcctgttccgtatttgggtaattttattt---cccatctttattttatcagtgaaaagcaatactcaa

upper sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT1G80670.1 (Arabidopsis thaliana), 5'ss of exon 7
ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatactttattttggaatgtcctttactgccacattcattaaacctagcttcttctgtataagcctatttttagtgtgcttcacaaacagattattta------
|| ||||| ||| |||||||||| ||||| || ||||||||  ||||  || |||| ||||||||||| ||||| |||||||||   |||  | ||   |||| || |  ||     ||   | ||   || ||     | || ||| | ||  |    |||||       || |||   |      
ACTGAGTTTAAGAGAATCCAATCCCCACTGAAGTACCAGACGAGGTGTGTTACTGCCTTCCCTGATCAGCAAGGTTTTTTGgtatgtcttcttatt--tatgttctgttgtgt----tttggttaattcagttttacaggaattagcttgttcgttagatgcttacattttaggttagacattgcaa

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|71310172|gb|DR791375.1|DR791375
EST:     AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|71319015|gb|DR796255.1|DR796255
EST:     AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|67019316|gb|CO448065.1|CO448065
EST:     AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|31355022|gb|CD439379.1|CD439379
EST:     AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|548062|gb|T25262.1|T25262
EST:     AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|71427496|gb|DR808546.1|DR808546
EST:     AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|32838237|gb|CD977915.1|CD977915
EST:     AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|78092605|gb|DV520979.1|DV520979
EST:     AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|78092604|gb|DV520978.1|DV520978
EST:     AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|71756690|gb|DR954627.1|DR954627
EST:     AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|78023897|gb|DV492284.1|DV492284
EST:     TGATCAACAAGGGTTTTT-                         GTTGGTTCAATAGAAGGAAGAGTGGGCGTTCATCATATCGATGACGCACAG
genomic: TGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|71765073|gb|DR963010.1|DR963010
EST:     AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|32789124|gb|CD941360.1|CD941360
EST:     AATACCAGACACGGAGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGGAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|32945537|gb|CF050356.1|CF050356
EST:     AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTG                         GTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAG
EST: gi|67024188|gb|CO452937.1|CO452937
EST:     AATACCAGACACGGTGCCTTGCTGCATTNCCTGATCA-CAAGGGGTTTTG                         GTTGGTTCA-TAGAAGGA-GAGTTGGGCGT-C-TCATATCGATGAC-CACA
genomic: AATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGG-CGTTCATCATATCGATGACGCACA

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: 47 (upstream exon), 49 (downstream exon)
Score: 261

ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAGCAAAGCAAAAACTTCACATTCAAATGCCACAGGGAAGGAAATGATATAT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 224

ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAGCAAAGCAAAAACTTCACATTCAAATGCCACAGGGAAGGAAATGATATAT


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 162

ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAGCAAAGCAAAAACTTCACATTCAAATGCCACAGGGAAGGAAATGATATAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 149

ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatacttt ... tcatttaaagGTTGGTTCAATAGAAGGAAGAGTTGGCGTTCATCATATCGATGACGCACAGCAAAGCAAAAACTTCACATTCAAATGCCACAGGGAAGGAAATGATATAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGGAGTTCAAGCGAATCCAATCACCACTAAAATACCAGACACGGTGCCTTGCTGCATTCCCTGATCAACAAGGGTTTTTGgtaatactttattttggaatgtcctttactgccacattcattaaacctagcttcttctgtataagcctatttttagtgtgcttcacaaacagattattta

- - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC