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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgcaccgttgattgtttcagtttatgatatgtagctgtgttgttccaaattctgaaacaattgctacgtgcgtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTACGGGCATC

Basic information

species Zea mays
transcript GRMZM2G099980_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170243_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 3'ss of exon 6
gtttgtgcaccgt--tgattgtttcagtttatg-atatgtagctgtgttgttccaaattctgaaacaattgctacgtgcgtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTACGGGCATC---
    ||  |   |  |  || | || |||| |  || |   |||    || |||    ||| || | |  |||  |  | |    ||||| || |||||||| ||||| ||||||||  ||||||| ||||| |||||||||||||| ||| |    |||||||| |||||||| ||| | || |||||   
----gtaaattataatttttttctcggtttgtttattttatgctagagtgctcc----tctaaagctagcgctttggacat----tcagACCGAAGAGGGGGGTCTTCGGCTTCCAATGCAAGGAAGGATGAATACAACTGGAGATATGATGCT---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|60349637|gb|DN216610.1|DN216610
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|5895715|gb|AW036961.1|AW036961
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|5006225|gb|AI712287.1|AI712287
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|71428991|gb|DR810041.1|DR810041
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCTACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|33770989|gb|CF273283.1|CF273283
EST:     GC-AATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGAATCT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCT
EST: gi|60349938|gb|DN216911.1|DN216911
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|67033833|gb|CO462582.1|CO462582
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCNACACNAGGGAAGATGAGTANCA-C
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTA-CAAC
EST: gi|71428990|gb|DR810040.1|DR810040
EST:     GCCAATCTTTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|76283944|gb|DV023512.1|DV023512
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|20513022|gb|BQ280208.1|BQ280208
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|26457465|gb|CA829048.1|CA829048
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|71427898|gb|DR808948.1|DR808948
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|71449093|gb|DR830143.1|DR830143
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCTAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|78025444|gb|DV493831.1|DV493831
EST:     GCCAATCTTTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|78544427|gb|DV621925.1|DV621925
EST:     GCCAATCTTTTTGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATTTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|32944273|gb|CF049092.1|CF049092
EST:     GCCAATCTCTTCGTCGTAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGT
EST: gi|60359114|gb|DN226087.1|DN226087
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|21626078|gb|BQ620999.1|BQ620999
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|211383597|gb|FL452880.1|FL452880
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|61118250|gb|DN559211.1|DN559211
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|31612035|gb|CD568657.1|CD568657
EST:     GCCAATCTCTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
EST: gi|12970923|gb|BG267226.1|BG267226
EST:     GCCAATCTTTTCGTCGCAGCAGGCATCAG                         ATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT
genomic: GCCAATCTCTTCGTCGCAGCAGGCATCAGgtttgtgcac ... gtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatgtagctgtgttgttccaaattctgaaacaattgctacgtgcgtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTACGGGCATC
                                              tactttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgcaccgttgattgtttcagtttatgatatgtagctgtgttgttccaaattctgaaacaattgctacgtgcgtactttcagATCGCAGAGGGGGATCTTCAGCTTCCAACACAAGGAAAGATGAGTACAACTGGAGATACGATACCACCGATGATATATCTGAAGAGGTGCTACGGGCATC

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