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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattgggtcctcacatcaacttaactacttaagtgtgaaaaggcagattgggtcctcaccattgtgttgcgcacatgacag

Basic information

species Zea mays
transcript GRMZM2G407044_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G407044_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os02g39570.1 (Oryza sativa), 5'ss of exon 11
CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattgggtcctcacatcaacttaactacttaagtgtgaaaaggcagattgggtcctcac-cattgtgttgcgcacatgacag----------------
|||||||| ||||| ||||||||||||||| |||||||| | |||||||| |||||||||||||||||| ||||  | ||    |  ||||  ||         |      |  | |   ||  | |     ||||    |      ||||                
CTTACTGGGGATCTCGACAAGATGGTTGCATTACAAAGGCTGTTGGAGCCTTATGGCATCTGTGAGgtatattgaattctttt-tgtacttttctttcacctcatccgtttgttgctcatgtggttatgtgatgtgaaatgatgtcaacagattatctgcgcaaata

upper sequence: GRMZM2G407044_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA08G13290.1 (Glycine max), 5'ss of exon 11
CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattgggtc--ctcacatcaacttaactacttaagtgt---gaaaaggcagattgggtcctcaccattg--tgttgcgcacatgacag----------
|||||||||||| | ||||||||||||||| | || || || || || ||||||||||| |||||||||  ||   |    |  | |  ||||| |    ||  | |   |   || ||| |||  |  |    |||   | || |  | ||  | |          
CTTACTGGAGATTTGGACAAGATGGTTGCATTGCAGAGATTGTTAGAACCATATGGCATTTGTGAGgtatgttttataagttttctttcacttaccatagtagatattttgctgagacag-ttgacttgtttaaattccttattccataaatctccggaaccgaatt

upper sequence: GRMZM2G407044_T01 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA05G30130.1 (Glycine max), 5'ss of exon 11
CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattgggtcc-tcacatcaacttaactacttaagtgt---gaaaaggcagattgggtcctcaccatt--gtgttgcgcaca-tgacag----------
|||||||||||| | ||||||||||||||| |||| || || || || ||||||||||| |||||||||  ||   |   |    || ||||| |    ||  | |   |   || ||| |||  |  |    |||  || || |  | | |  |||          
CTTACTGGAGATTTGGACAAGATGGTTGCATTACAGAGATTGTTAGAACCATATGGCATTTGTGAGgtatgttttataaattttttccacttaccatagtagatattttgctgagacag-ttgacttgtttaaattccgtattccataaacttccagagtcgaattt

upper sequence: GRMZM2G407044_T01 (Zea mays), 5'ss of exon 11
lower sequence: AT2G31810.2 (Arabidopsis thaliana), 5'ss of exon 11
CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattgggtcctc-acatcaacttaactacttaagtgtgaaaaggcagatt---gggtcctcaccattgtgttgcgcacat---gacag---------
|||||||| ||||| ||||||||||||||||| ||||||||||||||||| ||||| || ||||||||   ||  |   || || |  |  |        | |  | |    |   |||      | || |  ||  |  | |     |   || |          
CTTACTGGGGATCTAGACAAGATGGTTGCACTGCAAAGGTTATTGGAGCCCTATGGTATATGTGAGgtttgtttcgcaatctactttcatctcttagtgaatgcataaccccgtgaattcttaatttcttataatgatactccaattgttcggataaagtcccaaa

upper sequence: GRMZM2G407044_T01 (Zea mays), 5'ss of exon 11
lower sequence: Vv00s0220g00110.t01 (Vitis vinifera), 5'ss of exon 11
CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgt--------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|89253086|gb|DY624872.1|DY624872
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|211452062|gb|FL278247.1|FL278247
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|211122006|gb|FL444944.1|FL444944
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|24934868|gb|CA453086.1|CA453086
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|60338155|gb|DN205128.1|DN205128
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|211132732|gb|FL016680.1|FL016680
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|149087823|gb|EE287139.2|EE287139
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|211033398|gb|FL443777.1|FL443777
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|32940948|gb|CF045767.1|CF045767
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|211350147|gb|FL469218.1|FL469218
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|116818053|gb|EC860984.1|EC860984
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|211452063|gb|FL278248.1|FL278248
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|32793555|gb|CD945791.1|CD945791
EST:     ACAAGATGGTTGCACTACAAAGGGTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|78122763|gb|DV541147.1|DV541147
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|60343820|gb|DN210793.1|DN210793
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|60340849|gb|DN207822.1|DN207822
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|24773364|gb|CA408618.1|CA408618
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|211122005|gb|FL444943.1|FL444943
EST:     ACAAGATGGTTGCMCTACAAAGGTTATTGGAGCCATATGGCATYTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|148949306|gb|EC894757.2|EC894757
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|211452064|gb|FL278249.1|FL278249
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
EST: gi|211132731|gb|FL016679.1|FL016679
EST:     ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAG                         GTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC
genomic: ACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 74

CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCCAAGTACCTCCGCGGCTACTCTCTTCCACTGTAGCCTTGCAGTCGTGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 33

CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCCAAGTACCTCCGCGGCTACTCTCTTCCACTGTAGCCTTGCAGTCGTGATG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 19

CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCCAAGTACCTCCGCGGCTACTCTCTTCCACTGTAGCCTTGCAGTCGTGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 30

CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattggg ... cacatgacagGTCGCCAGAACTGGACGAGTAGCACTGGTCCGCGAATCGAAGGTGGACTCCAAGTACCTCCGCGGCTACTCTCTTCCACTGTAGCCTTGCAGTCGTGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTACTGGAGATCTTGACAAGATGGTTGCACTACAAAGGTTATTGGAGCCATATGGCATCTGTGAGgtagattgggtcctcacatcaacttaactacttaagtgtgaaaaggcagattgggtcctcaccattgtgttgcgcacatgacag

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