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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagataataaacatgtattttcattagtatttgtgtgttgattagtaaattaaattattgataccttgtggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGTCTTCTCTATGTTTTAACGGAGAAGCCCAAGATCGCTGGTGTGGATATTT

Basic information

species Zea mays
transcript GRMZM2G006069_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006069_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g02710.2 (Oryza sativa), 3'ss of exon 3
aagataataaacatgtattttcattagtatttgtgtgttgattagtaaattaaattattgataccttgtggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGTCTTCTCTATGTTTTAACGGAGAAGCCCAAGATCGCTGGTGTGGATATTT
|  | || |||      ||||   || | |||     |||  | ||||||||||||||||||  |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| || ||||||||||||   || |||||| |||| || |||||||  || || |||||||| ||| | |
agcaaaacaaaaccaactttttgataatttttacacattggcttgtaaattaaattattgatgtcttgcggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAGCTTATCACTTCTGAAGTTGCATTAAACCTCCTCTATATTTTGACCGAGAAGCGGAAAATTGCTGGTGTCGATCTAT

upper sequence: GRMZM2G006069_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G02070.1 (Glycine max), 3'ss of exon 2
----------------------------------------------------------------------------------aagataataaacatgtattttcattagt----------atttg---tgtgttgattagtaaatt-aaattattgataccttgtggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGTCTTCTCTATGTTTTAACGGAGAAGCCCAAGATCGCTGGTGTGGATATTT
                                                                                  |  || ||  | | | ||| | || ||           |||||   |||  ||  |||| |  | |||||  | ||  || ||  ||||||||||  | ||| ||||||||||||| |||||||||||||| ||||| || || ||| | ||| |||| ||| |  || | | | | ||||  ||  |    |   |  |  |  |||||    
gtaagttttcttcattcatttgtgttaatgataagaaaaggggaaaaattgtatgtaagaaaagggggaaaattatgataatataattatgtataggcattcttataagagaaagttataatttggcatgtagtggatagttatctcaaattggttat-tctggtttttttgacagat-gattccttgtcttccagAGTTTTGGGCAGCATGGAAGAGAGCTGATTACCACAGAACTTGCTTTAAGGATTTTGTCTATCTTAAGTGAAGAAAAAATTCTACCCAGCATGGATCAAG
















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|74244217|gb|DT652131.1|DT652131
EST:     ATCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATATCCTTCTG                         AGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGT
genomic: ATCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATATCCTTCTGgtcagtttcc ... tgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGT
EST: gi|211221619|gb|FL170902.1|FL170902
EST:     ATCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATATCCTTCTG                         AGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGT
genomic: ATCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATATCCTTCTGgtcagtttcc ... tgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGT
EST: gi|18178045|gb|BM379255.1|BM379255
EST:     ATCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATATCCTTCTG                         AGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGT
genomic: ATCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATATCCTTCTGgtcagtttcc ... tgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGT
EST: gi|211221621|gb|FL170904.1|FL170904
EST:     TCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATGATCCTTCTG                         AGCTTTGGGCAGCATGGCAGAGAACTTATCACCCTCCGAAGTYGCATTAC
genomic: TCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCAT-ATCCTTCTGgtcagtttcc ... tgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACC-TCCGAAGTTGCATTAC
EST: gi|211221616|gb|FL170899.1|FL170899
EST:     ATCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATATCCTTCTG                         AAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACG
genomic: ATCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATATCCTTCTGgtcagtttcc ... tgtcttccagA-GCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACG
EST: gi|76283051|gb|DV022619.1|DV022619
EST:     ATCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATATCCTTCTG                         AGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGT
genomic: ATCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATATCCTTCTGgtcagtttcc ... tgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGT
EST: gi|211221617|gb|FL170900.1|FL170900
EST:     ATCATGTGAAGGAGCGCATGGATNATGGCTCAAAAGTTCATATCCTTCTG                         AGCTTTGGGCAGCATGGCAGANAACTTATCACCTCCGAAGTTGCATTACGT
genomic: ATCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATATCCTTCTGgtcagtttcc ... tgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGT
EST: gi|211221620|gb|FL170903.1|FL170903
EST:     ATCATGTGAAGGAGCGCATGGATA-TGGCTCAAAAGTTCATATCCTTCTG                         AGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGT
genomic: ATCATGTGAAGGAGCGCATGGATAATGGCTCAAAAGTTCATATCCTTCTGgtcagtttcc ... tgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaattaaattattgataccttgtggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGTCTTCTCTATGTTTTAACGGAGAAGCCCAAGATCGCTGGTGTGGATATTT
                          ttttgac  putative branch site (score: 3)
                                            ttgtcttcc  putative PPT
     taaattattgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagataataaacatgtattttcattagtatttgtgtgttgattagtaaattaaattattgataccttgtggttttgacagaaaggttcattgtcttccagAGCTTTGGGCAGCATGGCAGAGAACTTATCACCTCCGAAGTTGCATTACGTCTTCTCTATGTTTTAACGGAGAAGCCCAAGATCGCTGGTGTGGATATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - -catgtat
- - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acagaaa