Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatttgcaataacttgtgactgactttgatatgtactattatgtagccgcctgtggtgttgctttccacggcgctgcacatgttttagatcttcatatcttgcgtgctataaatcacctttcttaatcagatgccatttcacctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAGGATAAGCGTTACAAGAACCGCGAGTTGCAGACCATGCGCCTTCTTGACC

Basic information

species Zea mays
transcript GRMZM2G024151_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G024151_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g14860.1 (Oryza sativa), 3'ss of exon 4
------------------------------------gttatttgcaataactt--gtgactgactt--tgatatgtactattatgtagccgcctgtggtgttgctttccacggcgctgcacatgttttagatcttcatatcttgcgtgctataaatcacctttct-----taatca-gatgccatttcacctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAGGATAAGCGTTACAAGAACCGCGAGTTGCAGACCATGCGCCTTCTTGACC
                                       ||   ||  ||  |  ||  || ||||      ||  ||| |  |    || | | |  |||    |  ||    | || | |     ||    |   |   |    ||   |||||   |||  |     ||||   |||  |||||   |  ||   |||| || ||| ||||||| |||||||| ||||| || ||||||||||||||||||||||| ||||||||||| ||| | ||||||||||||||||||||||
gttagttgcaacatctttgggttttcatatatttcaccaatcaccaggaagctaagtagctaacttaacatcattaactctactagcaccactttttttgt-atgtagcaaattgttg-atacacgataaccttctcttgttaagatgtcctaaatgttcttcatgtctgtaatagtgatatcattttgaccattttcagGCAAAATGTCTGGAGACAGGTGAGACAGTTGCTATCAAGAAGGTTCTTCAGGATAAGCGCTACAAGAACCGTGAGCTTCAGACCATGCGCCTTCTTGACC
















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|5566746|gb|AI881612.1|AI881612
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGNCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|19822195|gb|BQ048219.1|BQ048219
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|32928666|gb|CF033478.1|CF033478
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|32929341|gb|CF034153.1|CF034153
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|32928546|gb|CF033358.1|CF033358
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|26455791|gb|CA827374.1|CA827374
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|5566972|gb|AI881883.1|AI881883
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|6918384|gb|AW399914.1|AW399914
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGNTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|61117964|gb|DN558925.1|DN558925
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATTGGCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|5928717|gb|AW055934.1|AW055934
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|5268665|gb|AI770629.1|AI770629
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCA
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTG-TTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCA
EST: gi|22542189|gb|BU092627.1|BU092627
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|60349962|gb|DN216935.1|DN216935
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|33097218|gb|CF057178.1|CF057178
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|32863940|gb|CF003622.1|CF003622
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
EST: gi|30087106|gb|CB885314.1|CB885314
EST:     ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAG                         GCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG
genomic: ACATGGCTGAGCGCATTGTAGGTCAAGGTTCTTTTGGGATCGTCTTCCAGgttatttgca ... ctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgcgtgctataaatcacctttcttaatcagatgccatttcacctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAGGATAAGCGTTACAAGAACCGCGAGTTGCAGACCATGCGCCTTCTTGACC
                       tcttaat  putative branch site (score: 3)
                                       tttcacct  putative PPT
          tataaatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatttgcaataacttgtgactgactttgatatgtactattatgtagccgcctgtggtgttgctttccacggcgctgcacatgttttagatcttcatatcttgcgtgctataaatcacctttcttaatcagatgccatttcacctgttcatagGCTAAGTGTTTGGAGACGGGTGAGACTGTTGCCATAAAGAAGGTTCTTCAGGATAAGCGTTACAAGAACCGCGAGTTGCAGACCATGCGCCTTCTTGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC