Skip to another splice site:
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttttatccccctactgcctctcgcggcctcgttttcggctctgacctggttgtgtcgacgcag

Basic information

species Zea mays
transcript GRMZM2G019267_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019267_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 5'ss of exon 2
GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttttatccccctactgcctct------cgcggcctcgttttcgg---------ctctgac---------ctggttgtgtcgacgcag
|||||| |||||||| ||||||||||  || |||||||||||||||||||||||||||||||||||||||||||||||||| ||  |  ||    |||||  |  ||| |      | | ||| | | |||           ||||||          ||| |||  ||| |||||
GCAAGTTTACATGGCCAAGGAGACGGAGACGAACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGCgtatgaattcccccccccccccccctttttttttctccgccccttcttccaatttttcctctctgatgacgtgttgctgattgcctcggcgcag
















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|211438450|gb|FL012012.1|FL012012
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211438447|gb|FL012009.1|FL012009
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|89248442|gb|DY620228.1|DY620228
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|29130258|gb|CB380962.1|CB380962
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|148931632|gb|EC874770.2|EC874770
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|71774594|gb|DR972472.1|DR972472
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211438457|gb|FL012019.1|FL012019
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211435860|gb|FL012004.1|FL012004
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|76914973|gb|DV165773.1|DV165773
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211438453|gb|FL012015.1|FL012015
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|148962681|gb|EE013583.2|EE013583
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|148946782|gb|EC892051.2|EC892051
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211438455|gb|FL012017.1|FL012017
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|148938174|gb|EC882457.2|EC882457
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|110209027|gb|EC890924.1|EC890924
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACCCAAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211002224|gb|FL012020.1|FL012020
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211438454|gb|FL012016.1|FL012016
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211435853|gb|FL011997.1|FL011997
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211438448|gb|FL012010.1|FL012010
EST:     CGAGATCGTCGCGCTCAAGAAGATTCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: CGAGATCGTCGCGCTCAAGAAGAT-CCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211438445|gb|FL012007.1|FL012007
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211438446|gb|FL012008.1|FL012008
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211438452|gb|FL012014.1|FL012014
EST:     ACGAGATCGTCGCGCTCAATAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211438444|gb|FL012006.1|FL012006
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211435855|gb|FL011999.1|FL011999
EST:     CGANGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: CGA-GATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211435856|gb|FL012000.1|FL012000
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211435858|gb|FL012002.1|FL012002
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211002225|gb|FL012021.1|FL012021
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211435854|gb|FL011998.1|FL011998
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|148942610|gb|EC887630.2|EC887630
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC
EST: gi|211438456|gb|FL012018.1|FL012018
EST:     ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGG                         TTCCCGATCACCGCCATACGCGAGATCAAGATCCTGAAGAAGCTTCACCAC
genomic: ACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttt ... gtcgacgcagTTCCCGATCACCGCCATACGCGAGATCAAAATCCTGAAGAAGCTTCACCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGTGTACATGGCGAAGGAGACGGGCACCAACGAGATCGTCGCGCTCAAGAAGATCCGCATGGACAACGAGCGCGAAGGGgtgagtcttttatccccctactgcctctcgcggcctcgttttcggctctgacctggttgtgtcgacgcag

- - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA