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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacatgaatacaggcattatgtatctgcatgattctaatatcaaacttacgcttaatgagaaacaaaatctaaactgctcttatttaactttttgtcagGTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG

Basic information

species Glycine max
transcript GLYMA08G45210.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G45210.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os01g63270.2 (Oryza sativa), 3'ss of exon 12
tcacatgaatacaggcattatgtatctgcatgattctaata-tcaaacttacgcttaatgagaaacaaaatctaaactgctcttatttaactttttgtcagGTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG
 || ||    |     |||| |    |  |   || ||||  | | ||  |   || ||   ||     |  |||| ||      |     ||  | |||||| |||||  | || || |||||||| |||||||| |||||||| ||||| || ||||| || || ||||| || || || |||||||||||||||||||
-catatagtgagtaatattaagataatctagatttgtaatccttacacaaatatttgattgtaattttgaattaaaatgtggacctccttgttcctctcagGTGGTGTTCATTCCCAACTACAATGTATCTGTGGCCGAGGTGCTCATTCCTGGGAGTGAACTGTCACAGCACATCAGTACCGCAGGCATGGAAGCAAGTG

upper sequence: GLYMA08G45210.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 12
----------------------------------------tcacatgaatacaggcattatgtatctgcatgattctaatatcaaact--tacgcttaatgagaaacaaa------atctaaactgctcttatttaactttttgtcagGTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG
                                          |  || ||    |    |   |   |  | |  ||  |   | |||  |||    |    |   || |      |  |||| || |||| ||    ||  || |||||||| ||| |||||||||||||||| || ||||| || ||||| ||||| || || ||  | || ||||||||||| ||||| || |||||||||||||
gtatgaatggacgattgtcctttgaacccttcagaaagatcaatttgtatttgtgatccaccaaaaagagtaaccctttttctatactactacatacaggatggtccatatcatttacttaaagtgttctt-ttccttttcctgccagGTTGTCTTTATCCCAAATTACAATGTATCAGTGGCTGAAGTGCTTATTCCTGGTAGCGAATTGTCACAGCATATTAGTACTGCTGGTATGGAAGCAAGTG

upper sequence: GLYMA08G45210.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G46970.1 (Arabidopsis thaliana), 3'ss of exon 13
--tcacatgaatacaggcattatgtatctgcatgattctaatatcaaacttacgcttaatgagaaacaaaatctaaactgctcttatttaactt--tttgtcagGTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG
    |     || ||      ||  |||    |  | ||  |||     || ||   |  |    |  || | | ||||| |  ||    | ||  ||   ||||| || ||||| ||||| ||||||||  |||| || ||| |||| || || ||||||||||| ||||| || || ||||| ||||||||||| |||||||
gccaagcctgatgcaaatgcaataaatcactgttctccttttatt----ttccgaacatagcttgaagaagttttaactggttctaacgcatttgcttctccagGTGGTATTTGTTCCAAACTACAATGTCACTGTAGCGGAGATGCTAATACCCGGAAGTGAGCTATCTCAACACATCAGCACAGCAGGCATGGAGGCAAGTG

upper sequence: GLYMA08G45210.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 3'ss of exon 12
tcacatgaatacaggcattatgtatctgcatgattctaatatcaaacttacgcttaatgagaaacaaaatctaaactgctctta--tttaactttttgtcagGTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG
    |||  |       ||| |  | |  || ||||    |||    ||       ||  |  |||    || |      | ||  | |||     | ||||||||| ||||| |||||||| ||||||||||||||||||||||| ||||||||||||||| | || ||||| || ||||| || ||||||||||| ||||
-tgtatgttttggctttttaagcttttttat-attcagcaatcttttttttttagtatatgctacacttgctgatgcatccataactgtaaaaaaatttcagGTTGTTTTTGTTCCAAATTATAATGTGTCTGTGGCAGAGGTGCTTATTCCAGGAAGTGAGTTGTCACAGCACATCAGCACAGCTGGCATGGAAGCCAGTG

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|17963666|gb|BM270412.1|BM270412
EST:     ATGTCGGTGCTGTTGTCAACAGTGATCCTGAGGTCAACGGCTACTTGAAG                         GTTGTGTTTGTCCCAAATTACAATGTGTCT
genomic: ATGTCGGTGCTGTTGTCAACAGTGATCCTGAGGTCAACGGCTACTTGAAGgtaacttaat ... tttttgtcagGTTGTGTTTGTCCCAAATTACAATGTGTCT
EST: gi|22521900|gb|BU080711.1|BU080711
EST:     ATGTCGGTGCTGTTGTCAACAGTGATCCTGAGGTCA-CGGCTACTTGAAG                         GTTGTGTTTGTCC-AAATTACAATGTGTCTGTGGCAGAGGTGCTGAATTCC
genomic: -TGTCGGTGCTGTTGTCAACAGTGATCCTGAGGTCAACGGCTACTTGAAGgtaacttaat ... tttttgtcagGTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGA-TTCC
EST: gi|26047983|gb|CA784613.1|CA784613
EST:     ATGTCGGTGCTGTTGTCAACAGTGATCCTGAGGTCAACGGCTACTTGAAG                         GTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCA
genomic: ATGTCGGTGCTGTTGTCAACAGTGATCCTGAGGTCAACGGCTACTTGAAGgtaacttaat ... tttttgtcagGTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCA
EST: gi|15812555|gb|BI784830.1|BI784830
EST:     ATGTCGGTGCTGTTGTCAACAGTGATCCTGAGGTCAACGGCTACTTGAAG                         GTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCA
genomic: ATGTCGGTGCTGTTGTCAACAGTGATCCTGAGGTCAACGGCTACTTGAAGgtaacttaat ... tttttgtcagGTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttacgcttaatgagaaacaaaatctaaactgctcttatttaactttttgtcagGTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG
                                            ctttttgtc  CT-rich tract
                                  tcttatttaacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacatgaatacaggcattatgtatctgcatgattctaatatcaaacttacgcttaatgagaaacaaaatctaaactgctcttatttaactttttgtcagGTTGTGTTTGTCCCAAATTACAATGTGTCTGTGGCAGAGGTGCTGATTCCAGGAAGTGAGCTTTCTCAGCATATTAGCACTGCAGGCATGGAAGCAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- -catgaat
- - - - - acaggca
- - - - - - - - - - - - - -gcatgat
- - - - - - - - - - - - - - - - - - - - -tcaaact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa