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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCTAACGGTATCCTCTCTGTCAGTGCTGTGGACAAGGGTACAGGGAAGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctctagcaagcgatgtactgtcatgttttaagcgaggtacgtttctgatctgatgaattcgactttttgtatcaatcaaaaaccgtctag

Basic information

species Zea mays
transcript GRMZM2G079668_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079668_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os05g23740.1 (Oryza sativa), 5'ss of exon 7
TGATGCTAACGGTATCCTCTCTGTCAGTGCTGTGGACAAGGGTACAGGGAAGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctctagcaagcgatgtactgtcatgttttaagcgaggtacgtttctgatctgatgaattcgactttttgtatcaatcaaaaaccgtctag
 ||||| || || ||||| |||||||| || || ||||||||||| || ||||||||||| || || || |||||||| |||||  |||| ||||| |||||||||||| ||||| |            | || |   | |    |   |  ||||| ||    | |||||    |||| ||||||||| ||  ||
CGATGCCAATGGCATCCTTTCTGTCAGCGCCGTAGACAAGGGTACTGGAAAGAAGCAGGACATTACGATAACTGGTGCCAGCACATTGCCGAAGGATGAGgtatgtctcgagcaaactcgcagtcactgtcttattgactaatacctgctaggatcttata---ttgactt---atatccatcaaaaactgttcag
















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|13557623|gb|BG548979.1|BG548979
EST:     AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAG                         GTGGAGAGGATGGTTGGCGA
genomic: AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGA
EST: gi|149086883|gb|EE176427.2|EE176427
EST:     AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAG                         GTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
genomic: AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
EST: gi|32916947|gb|CF021759.1|CF021759
EST:     AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAG                         GTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
genomic: AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
EST: gi|13557622|gb|BG548978.1|BG548978
EST:     CACTCTGCCAAAGGACGAG                         GTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
genomic: CACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
EST: gi|78122878|gb|DV541262.1|DV541262
EST:     AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAG                         GTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
genomic: AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
EST: gi|32944827|gb|CF049646.1|CF049646
EST:     AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAG                         GTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
genomic: AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
EST: gi|211280572|gb|FL390095.1|FL390095
EST:     AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAG                         GTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
genomic: AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
EST: gi|31354353|gb|CD438710.1|CD438710
EST:     AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAG                         GTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
genomic: AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
EST: gi|33092395|gb|CF052389.1|CF052389
EST:     AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAG                         GTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
genomic: AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
EST: gi|31356114|gb|CD440471.1|CD440471
EST:     AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAG                         GTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
genomic: AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
EST: gi|67039401|gb|CO465656.1|CO465656
EST:     GAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCNCAA-GGACNAG                         GTGGAGAAGATGGTTGGCGAANCTGANAAGTTTGCAAAGGAGGACAAGGGA
genomic: GAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGC-CAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGG-A
EST: gi|67018243|gb|CO446992.1|CO446992
EST:     AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAG                         GTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
genomic: AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
EST: gi|67019123|gb|CO447872.1|CO447872
EST:     AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAG                         GTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG
genomic: AGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAG

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: 46 (upstream exon), 49 (downstream exon)
Score: 97

TGATGCTAACGGTATCCTCTCTGTCAGTGCTGTGGACAAGGGTACAGGGAAGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAGAAGCGAGACGCCATTGACACCAAGAACCAAGCCGAGTCGGTCATCTACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 399

TGATGCTAACGGTATCCTCTCTGTCAGTGCTGTGGACAAGGGTACAGGGAAGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAGAAGCGAGACGCCATTGACACCAAGAACCAAGCCGAGTCGGTCATCTACC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 43

TGATGCTAACGGTATCCTCTCTGTCAGTGCTGTGGACAAGGGTACAGGGAAGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAGAAGCGAGACGCCATTGACACCAAGAACCAAGCCGAGTCGGTCATCTACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 249

TGATGCTAACGGTATCCTCTCTGTCAGTGCTGTGGACAAGGGTACAGGGAAGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctct ... aaccgtctagGTGGAGAGGATGGTTGGCGAAGCTGAGAAGTTTGCAAAGGAGGACAAGGAGAAGCGAGACGCCATTGACACCAAGAACCAAGCCGAGTCGGTCATCTACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGATGCTAACGGTATCCTCTCTGTCAGTGCTGTGGACAAGGGTACAGGGAAGAAGCAGGATATCACAATTACTGGTGCTAGCACTCTGCCAAAGGACGAGgtatgtctctagcaagcgatgtactgtcatgttttaagcgaggtacgtttctgatctgatgaattcgactttttgtatcaatcaaaaaccgtctag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC