Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaatgtatgcagcgtttcggtagccttttattatcagctttattctaacattgtgtgctctttttctggaag

Basic information

species Zea mays
transcript GRMZM2G046587_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G046587_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g47600.2 (Oryza sativa), 5'ss of exon 5
TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtatttta---atgtatgcagcgtttcggtagccttttattatcagctttattctaacattgtgtgctcttttt--ctggaag
||||||||| || ||||||||||||||||| |||||||| ||||||||||||||||| ||||||||    |||||| |||| |||||| | ||||||||||||  | |   |||| ||     |||    |      ||| |  | | ||  ||||||||||  |  | || |   |||  ||
TGTTCTTTACTCATCTGTTGTTTACCCACACAACTATGGTTTCATTCCACGCACACTTTGTGAGGACGGTGACCCCATGGACGTCCTCGTCCTGATGCAGgtaactgatggatgtgtgtgtgttttttaaaagaaaatat-acaaacctt-ctctaacattgcttctttttctctcctgatag

upper sequence: GRMZM2G046587_T03 (Zea mays), 5'ss of exon 2
lower sequence: Vv04s0023g02050.t01 (Vitis vinifera), 5'ss of exon 4
TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaatgt---atgcagcgtttcggtagccttttattatcagctttattctaacattgtgtgctctttttctggaag-------------------------
||||||||| || || |||||||| |||||||||||||| ||||| || || ||  ||||||| || | ||| ||  |||||||||| || || ||||||||| | | || |   || |    || |   |  | |     || |  | | || ||   || |       | || |  ||                          
TGTTCTTTACTCATCAGTTGTTTATCCACATAACTATGGTTTCATCCCTCGAACCATCTGTGAAGACAGCGATCCTATGGATGTCCTGATTCTAATGCAGgtagtgtcatttgacataccatcttaccacaatcatgatacattacatcttttttatttttctaattaaatcttataaaaattcatcaattcgccctctcgtgtag
















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|19351061|gb|BM895593.1|BM895593
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|32849179|gb|CD988860.1|CD988860
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCGG                         GAACAAGTTGTCCCTGGGTGTTTCTTGCGAGCTCGTGCTATTTGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|32924525|gb|CF029337.1|CF029337
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|18168735|gb|BM338575.1|BM338575
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|76016905|gb|DT944075.1|DT944075
EST:     CCCCCTGGATGTCCTCATATTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: CCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|60348368|gb|DN215341.1|DN215341
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|149099848|gb|EE185900.2|EE185900
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|17931649|gb|BM268609.1|BM268609
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|74244614|gb|DT652528.1|DT652528
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|13126527|gb|BG317097.1|BG317097
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|60337363|gb|DN204336.1|DN204336
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|32924252|gb|CF029064.1|CF029064
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|32831285|gb|CD970963.1|CD970963
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCTTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
EST: gi|60354612|gb|DN221585.1|DN221585
EST:     GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGAAG                       
genomic: GCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGC---AGgtattttaat ... tttctgga
EST: gi|13126526|gb|BG317096.1|BG317096
EST:     GGATGTCCTCATACTGATGCAG                         GAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG
genomic: GGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATG

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: 245

TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 79

TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 72

TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 298

TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaat ... tttctggaagGAACAAGTTGTCCCTGGGTGTTTCCTGCGAGCTCGTGCTATTGGGCTCATGCCTATGATCGATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCTTTATTCCTCTGTTGTTTACCCACATAACTATGGCTTCATTCCACGCACACTCTGTGAGGATAACGACCCCCTGGATGTCCTCATACTGATGCAGgtattttaatgtatgcagcgtttcggtagccttttattatcagctttattctaacattgtgtgctctttttctggaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT