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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTGCATAATGGAGGGATCATTGATGATTGCAGCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattgggtcctcacatcaacttaactacttaagtgtgaaaaggcagattgggtcctcaccattgtgttgcgcacatgacag

Basic information

species Zea mays
transcript GRMZM2G407044_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G407044_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os02g39570.1 (Oryza sativa), 5'ss of exon 11
TCTTGCATAATGGAGGGATCATTGATGATTGCAGCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattgggtcctcacatcaacttaactacttaagtgtgaaaaggcagattgggtcctcac-cattgtgttgcgcacatgacag----------------
                                  |||||||| ||||| ||||||||||||||| |||||||| | |||||||| |||||||||||||||||| ||||  | ||    |  ||||  ||         |      |  | |   ||  | |     ||||    |      ||||                
----------------------------------CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaattctttt-tgtacttttctttcacctcatccgtttgttgctcatgtggttatgtgatgtgaaatgatgtcaacagattatctgcgcaaata

upper sequence: GRMZM2G407044_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA08G13290.1 (Glycine max), 5'ss of exon 11
TCTTGCATAATGGAGGGATCATTGATGATTGCAGCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattgggtc--ctcacatcaacttaactacttaagtgt---gaaaaggcagattgggtcctcaccattg--tgttgcgcacatgacag----------
                                  |||||||||||| | ||||||||||||||| | || || || || || ||||||||||| |||||||||  ||   |    |  | |  ||||| |    ||  | |   |   || ||| |||  |  |    |||   | || |  | ||  | |          
----------------------------------CTTACTGGAGATTTGGACAAGATGGTTGCATTGCAGAGATTGTTAGAACCATATGGCATTTGTGAGgtatgttttataagttttctttcacttaccatagtagatattttgctgagacag-ttgacttgtttaaattccttattccataaatctccggaaccgaatt

upper sequence: GRMZM2G407044_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA05G30130.1 (Glycine max), 5'ss of exon 11
TCTTGCATAATGGAGGGATCATTGATGATTGCAGCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattgggtcc-tcacatcaacttaactacttaagtgt---gaaaaggcagattgggtcctcaccatt--gtgttgcgcaca-tgacag----------
                                  |||||||||||| | ||||||||||||||| |||| || || || || ||||||||||| |||||||||  ||   |   |    || ||||| |    ||  | |   |   || ||| |||  |  |    |||  || || |  | | |  |||          
----------------------------------CTTACTGGAGATTTGGACAAGATGGTTGCATTACAGAGATTGTTAGAACCATATGGCATTTGTGAGgtatgttttataaattttttccacttaccatagtagatattttgctgagacag-ttgacttgtttaaattccgtattccataaacttccagagtcgaattt

upper sequence: GRMZM2G407044_T03 (Zea mays), 5'ss of exon 1
lower sequence: AT2G31810.2 (Arabidopsis thaliana), 5'ss of exon 11
TCTTGCATAATGGAGGGATCATTGATGATTGCAGCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattgggtcctc-acatcaacttaactacttaagtgtgaaaaggcagatt---gggtcctcaccattgtgttgcgcacat---gacag---------
                                  |||||||| ||||| ||||||||||||||||| ||||||||||||||||| ||||| || ||||||||   ||  |   || || |  |  |        | |  | |    |   |||      | || |  ||  |  | |     |   || |          
----------------------------------CTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAGgtttgtttcgcaatctactttcatctcttagtgaatgcataaccccgtgaattcttaatttcttataatgatactccaattgttcggataaagtcccaaa

upper sequence: GRMZM2G407044_T03 (Zea mays), 5'ss of exon 1
lower sequence: Vv00s0220g00110.t01 (Vitis vinifera), 5'ss of exon 11
TCTTGCATAATGGAGGGATCATTGATGATTGCAGCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgt--------aga---ttgggtcctcacatcaacttaactact--taagtgtgaaaaggcagattgggtcctcaccattg--tgttgcgcacatgacag-
                                  || || |||||| |  |||||||||||||||| || |||||||||||||| ||||| || ||||||||        |||   || | || |||| ||   |||||   |  | | | ||   || |  |||   |  |    |||      ||   | | |  || 
----------------------------------CTCACAGGAGATTTAAACAAGATGGTTGCACTGCAGAGGTTATTGGAGCCCTATGGGATTTGTGAGgtcagtctccagaatcttagttcttcacttcgtgttaacatttagttattttgctgagtcccattaaattttgcatattaacctctgtttatagggtaga

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|32793555|gb|CD945791.1|CD945791
EST:     ACAAGATGGTTGCACTACAAAGGGTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|148949306|gb|EC894757.2|EC894757
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|60343582|gb|DN210555.1|DN210555
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTGCATAATGGAGGGATCATTGATGATTGCAGCTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattgggtcctcacatcaacttaactacttaagtgtgaaaaggcagattgggtcctcaccattgtgttgcgcacatgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG