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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgcactggtgatcgtttcagtttgtagtatgtagctgtgttgttccaaattctgaaacaattgcccctggtacgtttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATC

Basic information

species Zea mays
transcript GRMZM2G151268_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151268_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 3'ss of exon 6
gtttgtgcactggtgatcgtttcagtttgtagtatgta-gctgtgttgttccaaattctgaaacaattgcccctggtacgtttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATC---
   |      |  |  |  | || ||||||    | || |||    || |||    ||| || | |  ||    |  |        |||||| || |||||||||||||| | ||||||  ||||||| ||||| |||||||||||||| ||| |    |||||||| |||||||| ||| |||| |||||   
--gtaaattataatttttttctcggtttgtttattttatgctagagtgctcc----tctaaagctagcgctttggaca--------ttcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACTGGAGATATGATGCT---GATGATATCTCTGAAGAAGTGTTGCGAGCATCAAG
















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|12971760|gb|BG267644.1|BG267644
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|4647161|gb|AI622236.1|AI622236
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|91049337|gb|EB159755.1|EB159755
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|32909956|gb|CF014768.1|CF014768
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|60348471|gb|DN215444.1|DN215444
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|74239381|gb|DT647295.1|DT647295
EST:     ACCTATCTTTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|21809549|gb|BQ667867.1|BQ667867
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|47961828|gb|CN844537.1|CN844537
EST:     ACCTATTTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|74239382|gb|DT647296.1|DT647296
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|94478768|gb|EB707726.1|EB707726
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCCGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|60399998|gb|DN232805.1|DN232805
EST:     ACCTATCTCTTCTTTGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|15323531|gb|BI478753.1|BI478753
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|211191649|gb|FL029190.1|FL029190
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|60400202|gb|DN233009.1|DN233009
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|45847355|gb|CN071298.1|CN071298
EST:     ACCTATCTCTTCTTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT
genomic: ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACT

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: 45 (upstream exon), 49 (downstream exon)
Score: 143

ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 123

ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 94

ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 106

ACCTATCTCTTCTTCGCAGCAGGCATCAGgtttgtgcac ... ttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagctgtgttgttccaaattctgaaacaattgcccctggtacgtttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATC
                                            tttactttc  CT-rich tract
                        aaacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgcactggtgatcgtttcagtttgtagtatgtagctgtgttgttccaaattctgaaacaattgcccctggtacgtttactttcagATCGCAGAGGGGGGTCTTCAGTTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTGCGGGCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC