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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actacgcattctgttcactgttatattttgatgttttcatgactcagtaggtttggtttgttgtagttatgattcaaaataatgttatacttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG

Basic information

species Zea mays
transcript GRMZM5G868168_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G868168_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g46740.1 (Oryza sativa), 3'ss of exon 3
----actacgcatt-ctgttcactgttatattttgatgttttcatgactcagt-aggtttggtttgttgt--agttatgattcaaaataatgttatacttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
    |||| | ||   |  | | |    ||||||    | ||   |  ||| | |  ||| |  ||  ||  ||||||| |||||| || | ||||        |||||||||||| || ||||| ||||| |||||||| ||||| || || ||||| |||||| | |||||||||||||||||||| || ||||| ||||||
agtcactaggaatcattacttagttgattattttataatcttttggtttcatttatttttagcctgcagttcagttatggttcaaattattattat--------gtagATTAGACACGGAGAAGCCGTTGGAATAATTGGTCCTTCGGGAACAGGAAAGTCAACTGTTTTGAAGGTTATGGCTGGGCTACTGGCTCCAGACAAG

upper sequence: GRMZM5G868168_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 2
-------actacgcattctgttcactgttatattttgatgttttcatgactcagtaggtttggtttgttgtagttatgattcaaaataatgttatacttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
          ||   || |       |  |  | |||  | || ||  |||   ||  | |  |||| |||  || |  |||    |  ||  ||| |   |  ||||| |  ||||||||||| ||||| |||||||| || || ||||| || ||||| ||  | |||||| |||| || || || |||||||||||||| 
ttaaatgtaaactagttgtaagtggggggaggtcttgcagatt-cagaacttgctaaatctt-tttgctgtt-ttttctttcttctttttgacataat---gaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA-

upper sequence: GRMZM5G868168_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA09G38730.1 (Glycine max), 3'ss of exon 2
actacgcattctgttcactgttatattttgat--gttttcatgactcagtag--gtttggt-ttgttgtagttatgattcaaaataatgttatacttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
      |||| | || |    |  |||| |    || ||  ||| |||| |   |||   | || |||  ||| |  ||     |  |  |    |  ||  |||||||||||||||||||| ||||| |||||||| ||||| ||||| || ||||| ||  | |||||| |||| ||||| || |||||||||||||| 
-----ccattattttgataaattcatttaggcaggtcttgctgattcagcaattgttaaatctttttgctgtttttttttttcttttttctgacataatgaatagATTAGACATGGTGAAGCTGTTGGAATAATTGGTCCTTCTGGGACCGGCAAATCTACAGTTTTGAAGATTATTGCTGGACTTCTTGCTCCGGACAAA

upper sequence: GRMZM5G868168_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 2
actacgcattctgttcactgttatattttgatgttttcatgactcagtaggtttggtttgttgtagttatgattcaaaataatgttat--acttttg----tgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
        || |||| || || ||      | | ||  |    |    |||        |           |  ||  | | | | |   | ||||     || ||||||||||||||||||| |||||| | ||||| ||||| || || ||||||||||| || || ||| |||||||||| || |||||||| ||||||
gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagacaccacattctaaccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG

upper sequence: GRMZM5G868168_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 2
-actacgcattctgttcactgttat-attttgatgttttcatgactcagtaggtttggtttgttgtagttatgattcaaaataatgttata-cttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
 | |     || |  || || || | || || |  ||  | ||| |   | | | || ||| |  |  |     || |   |  |  | || |   | | |||||||||||||| ||||| |||||||| ||||| ||||| || || || ||||||||  |  ||||| |||| || || || |||||||| ||||||
gagtggatttttttgtctctcttttcatatttagtttcccttgaattt-tggttatgttttatcat--tctctgtttattttcttactttaacccatttatagATTAGACATGGGGAAGCTGTTGGGATTATTGGGCCTTCTGGCACTGGGAAATCAACAGTTCTGAAGATTATTGCGGGACTTCTTGCTCCAGACAAG

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|50324151|gb|CO519277.1|CO519277
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|149004790|gb|EE039293.2|EE039293
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|19057652|gb|BM736319.1|BM736319
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|149078033|gb|EE166771.2|EE166771
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|211065956|gb|FK946601.1|FK946601
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|211065957|gb|FK946602.1|FK946602
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|78120174|gb|DV538558.1|DV538558
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|211380394|gb|FK976874.1|FK976874
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         A-----CATGGTGAAGCAGTTGGGA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGA
EST: gi|31350150|gb|CD434507.1|CD434507
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|33467141|gb|CF244190.1|CF244190
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|78103984|gb|DV522402.1|DV522402
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         A-----CATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|154130463|gb|EC872173.2|EC872173
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|76931706|gb|DV172823.1|DV172823
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|148986921|gb|EE030732.2|EE030732
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|149080766|gb|EE169831.2|EE169831
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         A-----CATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|91048130|gb|EB158548.1|EB158548
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|19436793|gb|BM953203.1|BM953203
EST:     TCCATAAGTCATTTGGAGAGAAACANGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
EST: gi|31356046|gb|CD440403.1|CD440403
EST:     TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAG                         ATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA
genomic: TCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 36

GAACAGACAGATTGATGATGACCGTGATGTACTCATAGAATGTAGAGATGTCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 71

GAACAGACAGATTGATGATGACCGTGATGTACTCATAGAATGTAGAGATGTCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

GAACAGACAGATTGATGATGACCGTGATGTACTCATAGAATGTAGAGATGTCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 60

GAACAGACAGATTGATGATGACCGTGATGTACTCATAGAATGTAGAGATGTCCATAAGTCATTTGGAGAGAAACAAGTATTAAGAGGTGTTAGTTTCAAGgtcagctttt ... ttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaggtttggtttgttgtagttatgattcaaaataatgttatacttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
                                          tactttt  CT-rich tract
                     ttatgattcaaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actacgcattctgttcactgttatattttgatgttttcatgactcagtaggtttggtttgttgtagttatgattcaaaataatgttatacttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - cattctg
- - - - - - -ttcactg
- - - - - - - - - - - - - - tgatgtt
- - - - - - - - - - - - - - - - - - -catgact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa