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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataatgaccacactaatattagaactgttatccaaaccctcaccactaaattgacttcacaacattgcagataattaattattctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA

Basic information

species Glycine max
transcript GLYMA02G12830.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G12830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g55080.1 (Oryza sativa), 3'ss of exon 2
tataatgaccaca--ctaatattagaactgttatccaaaccctcaccactaaattgacttcacaacattgcagataattaattattctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA
 | |   |||||   | |  |||   |   ||||  ||           | ||  | ||  || |     || ||||  ||  ||  |  | | |    ||||||||||||| ||||||| |||||||| ||||| ||||||||| | || || ||||||||||| |||||  |  | ||||| ||||| || || || || 
aagacacaccaccatccataattgccatcattattaaacatggatttgttcaa--ggctcaactaatcatcacataacaaaaaatggttttgcttgactcagGAGCTACTACAGGTGCACCAACAGCAAGTGCACTGTGAAGAAGCGCGTGGAGCGGTCTTCCGACGACCCTTCCGTCGTGATCACCACCTACGAGGGCCAG

upper sequence: GLYMA02G12830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g02060.1 (Oryza sativa), 3'ss of exon 2
--tataatgaccacactaatattagaactgttatccaaaccctca-ccactaaattgacttcacaacattgcagataattaattattctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA
    ||    ||| |||  | ||  || |   |   || |  |||  | ||   || | || |  |  |  ||  |   |   |||  | | | |     ||||||||||||| ||||||| |||||||| ||||||||||||||| |||| || || || ||||| |||||  |  | || || ||||| || || || |||
taattagcccccaaactttttttgcaaata--aattaatcaatcaatctcttggttaaattaattaattaacatgtgtgtgtatata-taaaaaaaaaaacagGAGCTACTACAGGTGCACGAACAGCAAGTGCACGGTGAAGAAGCGGGTGGAGCGCTCCTCCGACGACCCCTCCGTCGTCATCACCACCTACGAGGGCCAA

upper sequence: GLYMA02G12830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G018721_T01 (Zea mays), 3'ss of exon 2
----------tataatgaccacactaatattagaactgttatccaaaccctcaccact-aaattgacttcacaacattgcagataattaattatt--ctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA
            || ||  | ||       | |||||       |||     ||| || ||  |  ||    | |  |  |   |   | | |        |  |  | |||||||||||||||| ||||| |||||||| ||||||||||||||| | || || || || ||||| |||||  |  | || || ||||| || || || || 
gtacctactggctactgcacgcatggcatctggaactagctctgaaaattaaacccctcaagctagctagctagctctagaatcatcgagtcacggatgagtgtacgtagcagGAGCTACTACCGCTGCACCAACAGCAAGTGCACGGTGAAGAAGCGCGTGGAGCGCTCCTCCGACGACCCCTCCGTCGTCATCACCACCTACGAGGGCCAG

upper sequence: GLYMA02G12830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G143204_T03 (Zea mays), 3'ss of exon 2
tataatgaccacactaatatta-gaactgttatccaaaccctcaccactaaattgacttcacaacattgcagataattaattattctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA
 |   |        |   |||| | || |  |   | |   | |  |  | |   |  |  ||  | |    | ||||||        ||   ||  ||||||| |||||| ||||||| |||||||||||||| ||||||||| | || ||  |||| ||||| |||||  |  | || || ||||| || || || || 
-agtttttttttctttgcattacgtacggcaactaatataattattatgataactagctagcacaagtagtcaaaattaaggggctaaatttcttgagcagGAGTTACTACAGGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGACGACCCCTCCGTGGTCATCACCACCTACGAGGGCCAG

upper sequence: GLYMA02G12830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G143204_T02 (Zea mays), 3'ss of exon 2
tataatgaccacactaatatta-gaactgttatccaaaccctcaccactaaattgacttcacaacattgcagataattaattattctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA------------
              |   |||| | || |  |   | |   | |  |  | |   |  |  ||  | |    | ||||||        ||   ||  ||||||| |||||| ||||||| |||||||||||||| ||||||||| | || ||  |||| ||||| |||||  |  | || || ||||| || || || ||             
-------------tttgcattacgtacggcaactaatataattattatgataactagctagcacaagtagtcaaaattaaggggctaaatttcttgagcaggagttactacagGTGCACCAACAGCAAATGCACAGTGAAGAAGCGCGTGGAGAGGTCCTCCGACGACCCCTCCGTGGTCATCACCACCTACGAGGGCCAGCACTGCCACAGC

upper sequence: GLYMA02G12830.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G69310.1 (Arabidopsis thaliana), 3'ss of exon 2
tataatgaccacactaatattagaactgttatccaaaccctcaccactaaattgacttcacaacattgcagata-attaattatt-ctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA
              |  |||   |    | |      |  | | || |   ||   |     | ||   |  || |||  |||||  || |    | |  |||||||||||  | ||||||||||||| |||||||||||||||||| || ||||| || || || || ||| | || ||||| || ||||| ||||| |||
-------------gtcgtatataagtcatcagttt--ctttgatcattctcttagttaacggatatgcaacctatatttcttattgttgttgtgatatatagGAGCTACTATAGATGCACAAACAGCAGATGCACGGTGAAGAAGAGAGTAGAACGTTCATCAGATGATCCATCGATAGTGATCACAACATACGAAGGACAA

upper sequence: GLYMA02G12830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g00720.t01 (Vitis vinifera), 3'ss of exon 2
tataatgaccacactaatattagaac--tgttatccaaaccctcaccac-taaattgacttcacaacattgcagataattaattattctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA
    ||  |     |   |  | ||   ||||| | |       | ||  |||||||  ||   |       | |  ||||||| |  | | ||||||||||||||||| ||||||||||||||||||||||||||||||||||| || |||||||| || || ||||| || |  || || || || ||||||||||| |||
-gggatctcttgggttggaaaaaaatcttgttagctagttatatagcagataaattggatttgtattg--aaaaaagattaattttattcacacattttgcagGAGCTATTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAAAGAGTTGAACGCTCCTCGGAGGATCCCAGCATCGTAATCACTACATATGAAGGCCAA

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|21256035|gb|BQ452923.1|BQ452923
EST:     AGATGGCGGAAGTATGGTCAGAAGGCAGTTAAAAATAGTCCTTTCCCTAG                         GAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGA
genomic: AGATGGCGGAAGTATGGTCAGAAGGCAGTTAAAAATAGTCCTTTCCCTAGgtttacagct ... cattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actaaattgacttcacaacattgcagataattaattattctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA
                        agataattaattattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataatgaccacactaatattagaactgttatccaaaccctcaccactaaattgacttcacaacattgcagataattaattattctgatacattttgcagGAGCTACTACCGGTGCACAAACAGCAAATGCACGGTGAAGAAGAGGGTTGAACGGTCTTCCGAGGACCCAACAATTGTGATTACCACATATGAAGGGCAA

- - - - ccacact
- - - - - - - - - - - - - - - atccaaa
- - - - - - - - - - - - - - - - - - -ccctcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacaaca