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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatgtggggatcctctgttagcttggttctgtatttactttcgcacactgacttcagttagatcttcatttagatatttgattgtacttttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCATTATGGTGGCTTACAACAACAAGAAATATTACATAGATATTATAGAAACT

Basic information

species Glycine max
transcript GLYMA05G34630.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34630.2 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G114220_T01 (Zea mays), 3'ss of exon 7
ggatgtggggatcctctgttagcttggttctgtatttactttcgcacactgacttcagttagatcttcatttagatatttgattgtactttttta-----------tgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCATTATGGTGGCTTACAACAACAAGAAATATTACATAGATATTATAGAAACT
    ||  |||  |  |  ||   | || || || | |  || | | | |  ||||| ||   |   ||||  |   | | ||| |  ||  ||            | |||||| |||| ||| || || ||||| |||||||| || || ||||| ||||| ||||| || |||||||||||  ||||||| || |||||| | ||||| 
----gtaaggaaacctt--taaaattgtcctataatgatctt-gaaaattctcttcatttctcttggcattaggcgttatcattctcattacttgctgttaaattttccagCTTGGAAAAAACTTTAAGAAATTTCTCCTGCTTAACCACGGGAGACAGCATCATGGTAGCCTACAACAACAAACAATATTATATTGATATTGTTGAAACA

upper sequence: GLYMA05G34630.2 (Glycine max), 3'ss of exon 7
lower sequence: Vv03s0038g00750.t01 (Vitis vinifera), 3'ss of exon 7
----ggatgtgg-ggatcctctgttagcttggttctgtatttactttcgcacactgacttcagttagatcttcatttagatatttgattgtacttttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCATTATGGTGGCTTACAACAACAAGAAATATTACATAGATATTATAGAAACT
       | ||    |   |||| | |||    ||| | |    |   | | |       ||| || |   | |||||  | |||   | |  ||| | ||||||||| || |||||| | ||||| ||||||||||| || ||||||||||| || |||||||| || || || ||||||||||||||||||||| |||| || 
ttatctttttgataaaatatctgat-gctca--tctatgtcatttaatggatatgtgtagcaggtaca--ctaatttatcttttttcatttcttttataatgcagCTTGGAGACAACACTAAGGAACTTTTCCTGCTTAACCACTGGAGATAGTATCATGGTGGCATATAATAATAAGAAATATTACATAGATATTGTAGAGACA
















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|17023280|gb|BM094314.1|BM094314
EST:     TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|58014687|gb|CX701429.1|CX701429
EST:     TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|192322766|gb|FK014457.1|FK014457
EST:     TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TTACAGCCCCACACAAAAGACTTTTTGGATATTTCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
EST: gi|298168906|gb|HO009836.1|HO009836
EST:     TCCAATCCAAAAGCTAT                         CTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT
genomic: TCCAATCCAAAAGCTATgtgagttgac ... ttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactgacttcagttagatcttcatttagatatttgattgtacttttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCATTATGGTGGCTTACAACAACAAGAAATATTACATAGATATTATAGAAACT
                                        tactttttt  CT-rich tract
                       atttagatatttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatgtggggatcctctgttagcttggttctgtatttactttcgcacactgacttcagttagatcttcatttagatatttgattgtacttttttatgcagCTTAGAAACAACATTGAGGAATTTTTCCTGCTTGACTACTGGAGATAGCATTATGGTGGCTTACAACAACAAGAAATATTACATAGATATTATAGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
ggatgtg
- - - - - -tcctctg
- - - - - - - - - - - - -ggttctg
- - - - - - - - - - - - - - - - - - - - - cgcacac
- - - - - - - - - - - - - - - - - - - - - - - - - gacttca