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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacaaaattaaaaaaatacataaataaagaataaattgttattcctgaaaatgtggttattgactgtgtattattttattttcatatatcctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG

Basic information

species Glycine max
transcript GLYMA09G00430.2
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
-----taacaaaattaaaaaaatacataaataaagaataaatt-gttattcctgaaaatgtggttattgactgtgtattattttattttcatatatcctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
         || || || |   |  ||   |   |     ||  |||| |       || ||    || | |   |   || | ||      |   | |  |  |||| || ||||| || ||||||||||||||||| ||||||||  |||||||||| || ||||||||||| |||||||| || ||||| |||||| | || |
atgttccttaagataaacatgttgtattgttgttgttggcatgagttacttacttccatttgacctttcaat---tgacatctgatccctgca---cttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 18
taacaaaattaaaaaaatacataaataaagaataaattgttattcctgaaaatgt-ggttattgactgtgtattattttattttcatatatcctgcctca-gGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
     | || ||     | ||       |     |    |  ||  ||||  |||     |   | | || |||   |      ||  ||  || ||| | ||| || ||||| || |  |||||||||||||| |||||||| || |||||||| |||||||||||||| ||||| || || ||||| || ||||| || |
--ctcatatcaacctgttccactttcccacggccatgattattttttgaatgtgtcaaacacaaattttgaattgcctgtgacacaattactctcccttaagGATACGATGGCCCGGAAGCCTGCTGATCCTGAAGAAGAACTTCGGTGGATGTCTCAAGAAGTTCGTGGTTATGTAGAGGCTGTTTTGAACAGTTTGGCAG

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM5G870253_T01 (Zea mays), 3'ss of exon 2
taacaaaattaaaaaaatacataaataaagaataaattgt-tattcctgaaaatgtggttattgactgtgtattattttattttcatatatcctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
     |  |||   |||  |  ||  |     | | ||   | |  |  || |   | | | | | | |    |   || |     | | | |||  | |||| ||||||||||| || |||||||||||||| |||||||| ||||||||||| |||||||| ||||| ||||||||||| ||||| || ||||| ||||
-ttttatcttacctaaaggctaaagcatgttttcatttaaatgtatccaaacacaagatcacttattttactcttcattctacaactcttttctgtttaagGATACAATGGCTCGGAGGCCTGCTGATCCTGAAGAAGAACTTCGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTTTGAACAGTTTGGCTG

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 18
----------------------------------------------------------------------------taacaaaattaaaaaaat-acataaataaagaataaattgttattcctgaaaatgtggttattgactgtgtattattt---------------tattt--tcatatatcctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
                                                                            | |   | | |  |  || |  ||| |  ||      ||||   |  || |  ||    |||  |   | |   |||                 || |   |||| ||  | |   |||| || ||||| || ||||||||||||||||| ||||||||  |||||||||| |||||||||||||| ||||| || || ||||| |||||| | || |
gtaagttctagattaatacataattgtattgcatttctagctttcttttgtcgttttgctctactcaactaaatcatgatttattaaggatcatcatgtaatttcaggtccccttgtatattttggatgtgccaatataaatatttttccattaaaatacacaaactaacatctgaccatacatttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------------------taacaaaattaaaaaaat-acataaataaagaataaattgttattcctgaaaatgtggttattgactgtgtattattt----------------tattt--tcatatatcctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
                                                                             | |   | |    |  || |  ||| |  ||  |   ||||   |  || |  ||    |||  |   ||    |||                  || |  ||||| |   | |   ||||  | ||||| || ||||| ||||||||||| ||||||||  |||||||||| |||||||||||||| |||||||| || ||||| |||||| | || |
gtaagttctaggttaatacataattgaattgcatttctagctttccttttgtagttttgctttactcaattaaatcttgatttattagggatcatcatgtaatttcaggttcccttgtatgttttggatgtgccaatataaatactgctccattaaaatacacaaactaaacatctgatcatacacttttcgaaagGATGCTATGGCGCGGAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG

upper sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 18
lower sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 18
-----taacaaaattaaaaaaatacataaat-aaagaataaattgttattcctgaaaatgtggttattgactgtgtattattttattttcatatatcctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
     | |||   ||    |||   ||   | ||| ||  ||||    | ||  | | | |||||  |     ||||| ||| | |  ||  | ||      |||||| |||||||  ||||||||||| || || || |||||||| ||||||||||| |||||||| ||||| ||||||||||| |||||||| ||| | ||||
cctattgacatttttttttaaaattatgccttaaataagcaatttagttcccctatattatggttcct-----tgtatgattgt-tgatctgaaattgcttttcagGATACAATGGTCCGAAGACCTGCCGACCCAGAAGAAGAACTTCGATGGATGTCTCAAGAAGTGCGTGGCTATGTTGAAGCGGTTTTAAACAGTCTGGCTG

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|9820492|gb|BE556002.1|BE556002
EST:     CATCTGATGGTGGCCCTACAATGAGGCATAGCCTCTCTGATGGTTCCTTG                         GACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATG
genomic: CATCTGATGGTGGCCCTACAATGAGGCATAGCCTCTCTGATGGTTCCTTGgttagtttct ... cctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATG
EST: gi|5677594|gb|AI938724.1|AI938724
EST:     CATCTGATGGTGGCCCTACAATGAGGCATAGCCTCTCTGATGGTTCCTTG                         GACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATG
genomic: CATCTGATGGTGGCCCTACAATGAGGCATAGCCTCTCTGATGGTTCCTTGgttagtttct ... cctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATG
EST: gi|15000625|gb|BI321439.1|BI321439
EST:     CATCTGATGGTGGCCCTACAATGAGGCATAGCCTCTCTGATGGTTCCTTG                         GACACAATGGCTCTTTTACCTGCTGATCCTGAGGAAGAACTCCGATGGATG
genomic: CATCTGATGGTGGCCCTACAATGAGGCATAGCCTCTCTGATGGTTCCTTGgttagtttct ... cctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgaaaatgtggttattgactgtgtattattttattttcatatatcctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG
             tattgac  putative branch site (score: 2)
                                            tcctgcctc  putative PPT
                  actgtgtattatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taacaaaattaaaaaaatacataaataaagaataaattgttattcctgaaaatgtggttattgactgtgtattattttattttcatatatcctgcctcagGACACAATGGCTCGAAGACCTGCTGATCCTGAGGAAGAACTCCGATGGATGTCACAAGAAGTTCGTGGATATGTTGAAGCAGTTTTAAATAGTTTAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
-aacaaaa
- - - - - aaaaaaa
- - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - -tcctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - tgtggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gactgtg