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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctctctttctcatttagtcattttctttatgtatctcaataatatgaatatcgctgccgcctgccgtgctctttttctttaacttctctatctacgatgccgcag

Basic information

species Zea mays
transcript GRMZM2G042818_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042818_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g54860.1 (Oryza sativa), 5'ss of exon 13
GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctctctttctcatttagtcattttctttatgtatctcaataatatgaatatcgctgccgcctgccgtgctctttttctttaacttctctatctacgatgccgcag
|| ||||||||||| |||||||| ||||||||||||||||||||||   |||| | | || |            |||   || || | ||            |      |  | | || |||||   ||| || | |   | |||| | |   
GGAATTAGAGCTCTCAGCATCGACAAAGACAATGCCCCTAAGgttc---tctcatacacactc-----------ttaaacatgtctagaa----------atttttatttttcatactgttttt---taatttttgt---tgcgatacag---
















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|74240479|gb|DT648393.1|DT648393
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|15053507|gb|BI359052.1|BI359052
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGNCAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|32938089|gb|CF042908.1|CF042908
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|29544823|gb|CB605431.1|CB605431
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|37400624|gb|CF637668.1|CF637668
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGTAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|15057208|gb|BI361180.1|BI361180
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|166513361|gb|EG081639.1|EG081639
EST:     GGGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|148959114|gb|EC905254.2|EC905254
EST:     GGCATTAGAGCTTTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|45568357|gb|CK986026.1|CK986026
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|45847153|gb|CN071096.1|CN071096
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|37392700|gb|CF633603.1|CF633603
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACTGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|20336949|gb|BQ172579.1|BQ172579
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|45847757|gb|CN071700.1|CN071700
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|33092056|gb|CF052050.1|CF052050
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|32930057|gb|CF034869.1|CF034869
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTAC
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTAC
EST: gi|71304194|gb|DR788217.1|DR788217
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|29544214|gb|CB604594.1|CB604594
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|37383733|gb|CF628896.1|CF628896
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|40303747|gb|CK348134.1|CK348134
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|84970253|gb|DW468603.1|DW468603
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTCCCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|91053743|gb|EB164161.1|EB164161
EST:     GGCATTAGAGCTTTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|74239819|gb|DT647733.1|DT647733
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|211149870|gb|FL475634.1|FL475634
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|29131056|gb|CB381760.1|CB381760
EST:     GGCCTTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCCCTACCCCTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|37379687|gb|CF626591.1|CF626591
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
EST: gi|71762792|gb|DR960729.1|DR960729
EST:     GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAG                         TGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG
genomic: GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTG

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: 106

GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTGTTCCAGCCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 334

GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTGTTCCAGCCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 225

GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTGTTCCAGCCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 351

GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctct ... gatgccgcagTGGAATCCCACTACCCTTGAGGAGGTGAAGTACGAGGACATCGACCGTCTGTTCCAGCCGTTCAGTCCGGAGCTGGAACTTCAGGTCCCATCTGATGATT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCATTAGAGCTCTTAGCATCGATAAAGACAATGCCCCTAAGgttcctctctctttctcatttagtcattttctttatgtatctcaataatatgaatatcgctgccgcctgccgtgctctttttctttaacttctctatctacgatgccgcag

- - - AGAGCT