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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatttgcacttcatacaagcttaatttatgaatgtctataatgaaaattgattattttgaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCTAAGTTGAATTTTGATGATAATGCTGCATATCGCCAGAAAGAGATATTTT

Basic information

species Glycine max
transcript GLYMA10G04480.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 7
-------gtaagcatttgcacttcatacaa----gcttaatttatgaatg--tctataatga--aaattgattatttt----gaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCTAAGTTGAATTTTGATGATAATGCTGCATATCGCCAGAAAGAGATATTTT
        |||  | | | |  ||||        ||    ||||  | ||      | ||||  || |||   || ||    |   |||| |||||  | || ||||||||||| ||| |  |||| ||||||||||| |||||||| |||||||| |||||||| | | | ||||||||||||||| 
gtaatcaataacaaatggtatctcatttggaatggcccgctttaccactgcactggttatgactaatttggacatgttatgtgggtagATTAATCCTCTTGCTGAGACAGCTGACAACAAGCTGGTCGCTGCTGATGCAAAGTTGAACTTTGATGACAATGCTGCCTTTAGGCAGAAAGAGATATTTG

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G064695_T01 (Zea mays), 3'ss of exon 7
--------------------------gtaagcatttgcacttcat----acaagcttaatttatgaatgtctataatga--aaattgattattttgaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCTAAGTTGAATTTTGATGATAATGCTGCATATCGCCAGAAAGAGATATTTT
                           | |   |||  |  | ||    ||    || || | ||||| | ||   | |      || ||| | ||   |||| |||||  | |||||||||||||| ||| |  | || ||||||||||| || ||||| ||||||||||||||||||| | | |||||||| |||||| 
gtatgcagtgagaaaaggtcctcattttgatgctttttatcttattattacgttttttatctgtgaatttgtactgtaatttggatgcttaatgtgggtagATAAATCCTCTGGCGGAGACAGCTGACAACAAGCTTGTTGCTGCTGATGCAAAATTGAACTTTGATGATAATGCTGCATTTAGACAGAAAGAAATATTTG

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G20420.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------gtaagcatttgcacttcatacaag-cttaatttatgaatgtctataatgaaaatt--gattattttgaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCTAAGTTGAATTTTGATGATAATGCTGCATATCGCCAGAAAGAGATATTTT
            | |   | |    |  | |||   ||| | |||| ||| ||| |  |  ||  |   | | | |     ||||||||||| | ||||||||| |   ||| |||||||| ||||||||||| || ||||| || |||||||||||||| |  || || |||||| | ||  
gtgagttctctctcactgtcttttttctacacacttcttcagttataaatatcttttgttgaacctccaaatttctcttgtagATCAATCCCCTTGCGGAGACATCAACTAATCAATTGGTAGCTGCTGATGCCAAATTGAACTTCGATGATAATGCTGCGTTCCGACAAAAAGAGGTTTTCG

upper sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------gtaagcatttgcacttcat---acaagctta-atttatgaatgtctataatgaaaattgattat-tttgaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCTAAGTTGAATTTTGATGATAATGCTGCATATCGCCAGAAAGAGATATTTT
                               | |  |||  |  ||  |   | ||  ||| |||  |  ||    | |||   | |  ||| | |||||||||||||||||||| || |||||  | ||||||||||| || ||||||||||| |||||||| ||||| ||||||||||| | ||| |||||| | |||||| 
gtgagcataaactccctattttcaagctccatgaaaattgaccatttgtttgataattttagattcttttatcgaaagaatcttattctattttgtttgaacagATCAATCCCATCGCAGAGACTTCAGATAACCAATTAGTAGCTGCTGATGCAAAGTTGAACTTTGACGATAATGCTGCTTTTCGTCAGAAACATATATTTG

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|208201815|gb|GE000533.1|GE000533
EST:     TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAA                         ATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCT
genomic: TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAAgtaagcattt ... ttttgaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCT
EST: gi|17518793|gb|BM187835.1|BM187835
EST:     TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAA                         ATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCT
genomic: TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAAgtaagcattt ... ttttgaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCT
EST: gi|254325002|gb|GR834427.1|GR834427
EST:     TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAA                         ATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCT
genomic: TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAAgtaagcattt ... ttttgaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCT
EST: gi|15000418|gb|BI321232.1|BI321232
EST:     TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAA                         ATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCT
genomic: TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAAgtaagcattt ... ttttgaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCT
EST: gi|151406201|gb|EV276016.1|EV276016
EST:     TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAA                         ATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCT
genomic: TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAAgtaagcattt ... ttttgaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCT
EST: gi|151397308|gb|EV267181.1|EV267181
EST:     TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTT-GGAA                         ATCAATCCCATAGCGGAGACAGCTGATAAC
genomic: TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAAgtaagcattt ... ttttgaacagATCAATCCCATAGCGGAGACAGCTGATAAC
EST: gi|6727069|gb|AW311423.1|AW311423
EST:     TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAA                         ATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCT
genomic: TGAAGAATTTGTATAAACTTTTTGTTGATTGTGACTGCACTCTTTTGGAAgtaagcattt ... ttttgaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatacaagcttaatttatgaatgtctataatgaaaattgattattttgaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCTAAGTTGAATTTTGATGATAATGCTGCATATCGCCAGAAAGAGATATTTT
                                    aattgat  putative branch site (score: 4)
                                          ttatttt  CT-rich tract
           ttaatttatgaatgtc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatttgcacttcatacaagcttaatttatgaatgtctataatgaaaattgattattttgaacagATCAATCCCATAGCGGAGACAGCTGATAACCAATTGGTGGCTGCTGATGCTAAGTTGAATTTTGATGATAATGCTGCATATCGCCAGAAAGAGATATTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA