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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGACATGCTGAGGGAGCGAGGCCTGCATCACGACTACGTGACTGCGATGCTGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggctttgctttgattcgctcttccccctttcaccttgcatacgccgatgactgacgcgaggattcgcccag

Basic information

species Zea mays
transcript GRMZM2G444692_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G444692_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os10g26145.1 (Oryza sativa), 5'ss of exon 11
GGACATGCTGAGGGAGCGAGGCCTGCATCACGACTACGTGACTGCGATGCTGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggctttgctttgattcgctc-ttccccctttcaccttgcatacgccgatgactgacgcgaggattcgcccag----------------------
|||||||||||| ||||| ||| |||| || |||||||| |||||| | |||||||| || ||| || ||||||| || ||||| || |||||||||||||| ||    |      ||   | | | || | ||  ||    | || |     |  |               |  |                        
GGACATGCTGAGAGAGCGGGGCTTGCACCATGACTACGTCACTGCGTTACTGCAAGACGGATACCACCTGGAGGCTCTTCGCTACGCTAGAAAATACAAGgtactcttttgccaactggcgcacacgtttctcccatcttgctccaaatttataaaatcactatatcatcatgttcgtatttcctatgcattgcaagttt
















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|211272780|gb|FL461440.1|FL461440
EST:     TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTYTGGAGAAAGCCCTGGCGAAGAAC
genomic: TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
EST: gi|211085836|gb|FL083838.1|FL083838
EST:     TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
genomic: TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
EST: gi|71433592|gb|DR814642.1|DR814642
EST:     TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
genomic: TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
EST: gi|71436759|gb|DR817809.1|DR817809
EST:     TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
genomic: TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
EST: gi|4804009|gb|AI665875.1|AI665875
EST:     TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
genomic: TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
EST: gi|116817309|gb|EC860144.1|EC860144
EST:     TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGACTGCCCTATTTACTGGAGAAAGCCCTGGCGAAGAA
genomic: TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTT-CTGGAGAAAGCCCTGGCGAAGAA
EST: gi|78024231|gb|DV492618.1|DV492618
EST:     TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
genomic: TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
EST: gi|211085835|gb|FL083837.1|FL083837
EST:     TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCAAAGAAC
genomic: TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
EST: gi|60397571|gb|DN230387.1|DN230387
EST:     TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
genomic: TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
EST: gi|211085834|gb|FL083836.1|FL083836
EST:     TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
genomic: TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
EST: gi|166669898|gb|EG170764.1|EG170764
EST:     CTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
genomic: CTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
EST: gi|71433593|gb|DR814643.1|DR814643
EST:     TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
genomic: TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
EST: gi|71428498|gb|DR809548.1|DR809548
EST:     TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
genomic: TGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
EST: gi|32849841|gb|CD989522.1|CD989522
EST:     ACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAG                         GTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC
genomic: ACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAAC

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: 199

GGACATGCTGAGGGAGCGAGGCCTGCATCACGACTACGTGACTGCGATGCTGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAACAGCGCCCACAACCTGGCTGCAGTGCTGAGCTTCTTCTGCGAGTTCACTC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 253

GGACATGCTGAGGGAGCGAGGCCTGCATCACGACTACGTGACTGCGATGCTGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAACAGCGCCCACAACCTGGCTGCAGTGCTGAGCTTCTTCTGCGAGTTCACTC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 191

GGACATGCTGAGGGAGCGAGGCCTGCATCACGACTACGTGACTGCGATGCTGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAACAGCGCCCACAACCTGGCTGCAGTGCTGAGCTTCTTCTGCGAGTTCACTC


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 162

GGACATGCTGAGGGAGCGAGGCCTGCATCACGACTACGTGACTGCGATGCTGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggct ... attcgcccagGTGATCACCGTGCAGCCTGCCCTATTTCTGGAGAAAGCCCTGGCGAAGAACAGCGCCCACAACCTGGCTGCAGTGCTGAGCTTCTTCTGCGAGTTCACTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGACATGCTGAGGGAGCGAGGCCTGCATCACGACTACGTGACTGCGATGCTGCAAGATGGGTACTACTTGGAGGCCCTGCGCTATGCCAGAAAATACAAGgtccttggctttgctttgattcgctcttccccctttcaccttgcatacgccgatgactgacgcgaggattcgcccag

- - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG