Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgccttcgctcctcttgattcaagagatggtgcattcaaatgattttgtactgttgaaatcttttaccccatcgtgacgttcgtagctttttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTCCT

Basic information

species Zea mays
transcript GRMZM2G495626_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G495626_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g67160.1 (Oryza sativa), 3'ss of exon 4
ttgccttcgctcctcttgattcaagagatggtgcattcaaatgattttgtactgttgaaat-cttttaccccatcgtgacgttcgtagctttttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTCCT
|   |  |     || |  ||         ||   | |      ||  ||||     | || ||    || |||  |||   ||||| || ||  || |||||||||||| | || | || ||||| ||||| |||||||| ||||||||||||||||||||||| |||||     
taagcagcatatatcatacttttgcttcaagtttttcccttgctttcagtacaaaaaacatactgcctcctcattttgattctcgta-ctgttctatacagCTGAAATGGTCAGAAGACAAGCTCTTTTTCCAGGTGACTCTGAGTTGCAACAGTTGCTTCACATTTTCAG-----
















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|149101462|gb|EE187582.2|EE187582
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|71431608|gb|DR812658.1|DR812658
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|213167909|gb|FM191321.1|FM191321
EST:     CACATTACTNNACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: CACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|30306650|gb|CD001323.1|CD001323
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|71771339|gb|DR969276.1|DR969276
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTG
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTG
EST: gi|71450236|gb|DR831286.1|DR831286
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|91055879|gb|EB166297.1|EB166297
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|87157025|gb|DY401814.1|DY401814
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGGCCGACGGCAGGCTCTCTT
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTT
EST: gi|87155782|gb|DY400571.1|DY400571
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|76294289|gb|DV033857.1|DV033857
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|50328765|gb|CO523891.1|CO523891
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|91872387|gb|EB402344.1|EB402344
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCCTTCCTGGTGACTCGGAGTT-CAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|5005601|gb|AI711663.1|AI711663
EST:     AACACATTGCTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|74238746|gb|DT646660.1|DT646660
EST:     CAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: CAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|211362664|gb|FL128442.1|FL128442
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|71450237|gb|DR831287.1|DR831287
EST:     AACACATTACTCTACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|110195341|gb|EC877238.1|EC877238
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|76289583|gb|DV029151.1|DV029151
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|50336412|gb|CO531538.1|CO531538
EST:     ACACATTACTCAACTGGCGTTGATATGTGGTTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: ACACATTACTCAACTGGCGTTGATATGTGG-TCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|60343112|gb|DN210085.1|DN210085
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|76908586|gb|DV163013.1|DV163013
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|211301653|gb|FL434049.1|FL434049
EST:     GATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: GATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|91878647|gb|EB408604.1|EB408604
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCGGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|149110995|gb|EE294494.2|EE294494
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|71313275|gb|DR793171.1|DR793171
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|71313277|gb|DR793172.1|DR793172
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|71431609|gb|DR812659.1|DR812659
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTT
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTT
EST: gi|22935988|gb|BU572263.1|BU572263
EST:     AACACATTACTCAACTGGCGTTGATATG-GGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGG-GACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
EST: gi|91873993|gb|EB403950.1|EB403950
EST:     AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTG                         CTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC
genomic: AACACATTACTCAACTGGCGTTGATATGTGGTCTGTTGGATGCATCTTTGgtaagtctgt ... tttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtactgttgaaatcttttaccccatcgtgacgttcgtagctttttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTCCT
                                            ttttaat  putative branch site (score: 3)
                                          cttttt  CT-rich tract
            aaatctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgccttcgctcctcttgattcaagagatggtgcattcaaatgattttgtactgttgaaatcttttaccccatcgtgacgttcgtagctttttaatgcagCTGAAATGGCCCGACGGCAGGCTCTCTTTCCTGGTGACTCGGAGTTGCAACAGTTGCTTCACATCTTCAGGTCCT

-tgccttc
- - - - gctcctc
- - - - - - - - tgattca
- - - - - - - - - - - - - - - -tgcattc
- - - - - - - - - - - - - - - - - - - - - - - - - -ctgttga