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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaatataggaaaaggatattaaacttgttctggttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA

Basic information

species Glycine max
transcript GLYMA02G47860.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 4
gtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaat-ataggaaaaggatattaaacttgttctggtt-----attgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
         ||| |           |    ||||| |  ||| |||| || |||| |||   |   |||  |   |||||| |  ||       ||||||  ||||| |||| ||||||   |||| |||  |||| |||||| ||||||| || ||||| |||||||||||||||||||  || || ||| | |||||
--------gttacagttcatgaggcagcc-tttctataaattctgttcaagaaattatatttacctgatcatgggcttgtttttatttcctttctgcagCGACAATGTTTGCAGCACAGTCAATTCTATTGGGCATCAATGATATTGTTGTAGCCGGTGGCATGGAAAGCATGTCTAATGCTCCAAAATACATTGCTGA

upper sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 4
gtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaatataggaaaaggatatta----aacttgttctggttat-----------tgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
    ||||      || |||  ||| | |||   | |||| | || | | |    | || |    || ||||    | | || ||| ||| |           ||||||| | ||| |||| ||||||   ||||||||  | || |||||| |||||||||||||||| |||||||||||||| ||||  || |||||| | |||||
----gtttgaatcgaattta--tctgtctgtccttgtgtactctgctcagagttcacagaagtgagagattacctgaccatgctcttgttttcctttcctatatgcagCTACTATGTTTGCAGCACAGTCAATTCAATTGGGTATCAATGATATTGTTGTGGCTGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA

upper sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 4
---------------gtttgtttat---tataaaattaattctatttgtt--tctttgtattttg----tttaaaaaatatagg-aaaaggatattaa------acttgttctggttat----tgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
                | | |  ||   | || |||| || ||  ||| |  || |||| ||||     | | ||   |  |||     |  ||| |       | ||  |||    |     ||||||| | ||| | || ||||||   |||||  |  | || |||||| |||||||||| ||||| |||||||||||||| ||||  || |||||| | |||||
gtctgaagctaattcatctatccatgtttgtataattgat-ctgcttgctgttcattgttttttacacatgtgaagtgttcaggtgtgtgtgtatcatctgaccaattactctctgcacactctgcagCTACTATGTTCGCCGCACAGTCAATTCAGCTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA

upper sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 2
---gtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaatataggaaaaggata---ttaaacttgttctggttat-tgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
                            | |  | |  |   |  | |   ||   | | |  |   |   |   | |  ||| |  |   ||| ||||||| | ||| |||| ||||||   |||||| |  | || |||||| |||||||||| ||||| |||||||||||||| ||||  || |||||| | |||||
nnnnnnnnnnnnnnnnnnnnnnnnnnnnaatactctgctcacaggtcgcagaagtgacagattatctgatcatgctcaggcttttctttcctatatgcagCTACTATGTTTGCAGCACAGTCAATTCAACTGGGTATCAATGATATTGTTGTGGCAGGTGGCATGGAAAGCATGTCCAATGCCCCAAAGTACATTGCTGA

upper sequence: GLYMA02G47860.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 4
--gtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaatataggaaaaggatattaaactt---gttctggttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
  |    | ||| || | |  ||    || | || || | |           | | || ||   ||    ||    |||    | ||||| ||||||||  ||||||| || ||||||||||| || ||  |  | |||||| |||||||| |||||||||||||||||||||||||||| || || ||||| || ||
gtgccactctatcatcaga--aacagcatcttttcctctttccccaaaactgacactaaagtgtaatatcatggttcttttaatgctggtaattgcagCAACAATGCTCGCAGCACAGAGTATCCAGTTGGGTGTCAATGATATTGTTGTGTCTGGTGGTATGGAAAGCATGTCTAATGTGCCTAAATACCTAGCAGA

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|298197389|gb|HO044868.1|HO044868
EST:     TTCAGTAATCTGTACTACTGTTAACAAAGTTTGTGCATCAGGAATGAAAG                         CTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTG
genomic: TTCAGTAATCTGTACTACTGTTAACAAAGTTTGTGCATCAGGAATGAAAGgtttgtttat ... gttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTG
EST: gi|298168588|gb|HO009518.1|HO009518
EST:     TTCAGTAATCTGTACTACTGTTAACAAAGTTTGTGCACCAGGAATGAAAG                         CTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTG
genomic: TTCAGTAATCTGTACTACTGTTAACAAAGTTTGTGCATCAGGAATGAAAGgtttgtttat ... gttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttgtttaaaaaatataggaaaaggatattaaacttgttctggttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA
       tttaaaaaatatagga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttattataaaattaattctatttgtttctttgtattttgtttaaaaaatataggaaaaggatattaaacttgttctggttattgcagCTGCAATGCTTGCTGCACAGAGTATTCAATTAAGCATAAATGATGTTGTTGTGGCTGGTGGTATGGAAAGCATGTCTAATGTACCCAAGTACCTGGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG