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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctcacacaaataaatgaaaccttttcgatattttatcttaatcaaagtcattatttgctaccatgatgaaattgtgatcactccaagtgtatattggtgtgaattggtcctttaatcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAG

Basic information

species Zea mays
transcript GRMZM2G160569_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160569_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g44070.2 (Oryza sativa), 3'ss of exon 6
gtatgctcacacaaataaatgaaacct-tttcgatattttatcttaatcaaagtcattatt-tgctaccatgatgaaattgtgatcactccaagtgtatattggtgtga-attggtcctttaatcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAG---------------------------------------
||| | ||||| | | |||||| || |  || |||    | | |    |  | || ||  | ||     ||  ||  |  || |   ||  ||   | |  |  |  |  || | |    | | |||||||||||||||||||||||| |  || ||||||||   ||| |||||||| |||||||||||||||                                       
gtaagttcacatatagaaatgagacttgctttgatgcagtttttcttgcccattctttgctatggatgaatactggtagagtaaaagct--aatcatctgatattacgttatggatttaattaccatttgcagTGTTGATGTTTCTGGGCAACGAGAAATGAGGGACTTCTTCAATGGTATTGTGAGATTGCAGGTATCTGCCACTGTCCACCATGTTATGATACTTCTGTTC

upper sequence: GRMZM2G160569_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os07g44070.1 (Oryza sativa), 3'ss of exon 6
gtatgctcacacaaataaatgaaacct-tttcgatattttatcttaatcaaagtcattatt-tgctaccatgatgaaattgtgatcactccaagtgtatattggtgtga-attggtcctttaatcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAG
||| | ||||| | | |||||| || |  || |||    | | |    |  | || ||  | ||     ||  ||  |  || |   ||  ||   | |  |  |  |  || | |    | | |||||||||||||||||||||||| |  || ||||||||   ||| |||||||| |||||||||||||||
gtaagttcacatatagaaatgagacttgctttgatgcagtttttcttgcccattctttgctatggatgaatactggtagagtaaaagct--aatcatctgatattacgttatggatttaattaccatttgcagTGTTGATGTTTCTGGGCAACGAGAAATGAGGGACTTCTTCAATGGTATTGTGAGATTGCAG
















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|67013089|gb|CO441838.1|CO441838
EST:     TCGAATACCAGAGTCAAATGCCTAGCTGACGCTGGAATGTTTCTTGACAC                         TGTTGATGTCTCTGGCCGTCGG
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGG
EST: gi|149110301|gb|EE190341.2|EE190341
EST:     TCGAATACCAGAGTCNAATGCCTAGCTGATGCTGGAATGTTTCTTGACAC                         TGTTGATGTTTCTGGGCGTCGGGAAATGAGATCCTTTTT
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTT
EST: gi|211266712|gb|FL294975.1|FL294975
EST:     CAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACAC                         TGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGT
genomic: CAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGT
EST: gi|67018103|gb|CO446852.1|CO446852
EST:     TCGAATACCAGAGTCAAATGCCTAGCTGACGCTGGAATGTTTCTTGACAC                         TGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGT
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGT
EST: gi|148980469|gb|EE027156.2|EE027156
EST:     TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACAC                         TGTTGATGTTTC
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTC
EST: gi|31356050|gb|CD440407.1|CD440407
EST:     TCAAATACCAGAGTCAAATGCTTAGCTGATGCTGGAATGTTTCTTGACAC                         TGTTGATGTTTCTGGCCGCCGGGAAATGAGATCCTTTTTCAATGGTATTGT
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGT
EST: gi|93016717|gb|EB642237.1|EB642237
EST:     TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGGATGTTTCTTGACAC                         TGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTT
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTT
EST: gi|149066716|gb|EE286857.2|EE286857
EST:     TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACAC                         TGTTGATGTTTCTGGC
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGC
EST: gi|149085225|gb|EE174733.2|EE174733
EST:     TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACAC                         TGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGT
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGT
EST: gi|148953388|gb|EE152882.2|EE152882
EST:     TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACAC                         TGTTGATGTTTCTGGCCGTCGG
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGG
EST: gi|149028342|gb|EE286117.2|EE286117
EST:     TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGGATGTTTCTTGACAC                         TGTTGATGTTTCTG
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTG
EST: gi|149101142|gb|EE187250.2|EE187250
EST:     TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACAC                         TGTTGATGTTTCTGGCCGTCGGGAA-TGAGATCCTTTT
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTT
EST: gi|78075695|gb|DV504129.1|DV504129
EST:     TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGGATGTTTCTTGACAC                         TGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTT
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTT
EST: gi|32837541|gb|CD977219.1|CD977219
EST:     TCAAATACCAGAGTCAAATGCTTAGCTGATGCTGGAATGTTTCTTGACAC                         TGTTGATGTTTCTGGCCGCCGGGAAATGAGATCCTTTTTCAATGGTATTGT
genomic: TCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGT

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), 47 (downstream exon)
Score: 115

GTGGTGTTTCTACCATACTTCACTGTGATGAATTCCATGGATTGTTTCCCTCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 193

GTGGTGTTTCTACCATACTTCACTGTGATGAATTCCATGGATTGTTTCCCTCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

GTGGTGTTTCTACCATACTTCACTGTGATGAATTCCATGGATTGTTTCCCTCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 245

GTGGTGTTTCTACCATACTTCACTGTGATGAATTCCATGGATTGTTTCCCTCGAATACCAGAGTCAAATGCCTAGCTGATGCTGGAATGTTTCTTGACACgtatgctcac ... tcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtgatcactccaagtgtatattggtgtgaattggtcctttaatcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAG
                                       ctttaat  putative branch site (score: 245)
                                        tttaatcattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgctcacacaaataaatgaaaccttttcgatattttatcttaatcaaagtcattatttgctaccatgatgaaattgtgatcactccaagtgtatattggtgtgaattggtcctttaatcatttgcagTGTTGATGTTTCTGGCCGTCGGGAAATGAGATCCTTTTTCAATGGCATTGTGAGATTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC