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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagatacccatgaccatgagtaacaatcaattacatgatatctcgagttatttgctatttactcccattttgaatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA

Basic information

species Zea mays
transcript GRMZM2G006977_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 4
----tagatacccatgaccatgagtaacaatcaattacatgatatctcgagttatttgctatttactcccattttgaatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA
    ||| |  |  |||   ||    || ||| ||| ||||   ||   |||| | ||| | ||  || |      |||||  | || |   || |  ||  ||||||| ||||| ||||||||||| || |||||||| |||||||||||||| || ||||||||||| ||||||||||| ||||| ||||| || |||||||
aatttagttgtct-tgagt-tgtactaccatccatttcatgccctcat-agttctatgc-actttttcactcccaaaatttctcactgtgctatctgtttgcagGTGGCAAAAGAAAGTGCTGACGTGATTATTCTTGACGACAACTTCTCCACTATAGTCACTGTTGCTAAATGGGGTCGGTCAGTGTACATTAATATTCAGA

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 5
-tagatacccatgaccatgagtaacaatcaattacatgatatctcgagttat-ttgctatttactcccattttgaatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA
  |  ||      |||| ||  || |   |   | ||  |   || | | || ||  | ||      ||    ||||       || |  || |   |  |||| || ||||| ||||| || ||||| ||||| ||||| || ||||||||||| || || || || |||||||| || ||||||||||| || ||||| |
ccaattatttgaaacca-gaagaagagaaagggaaattttga-tcaaatgatcttattgttctaaagcaaggagaatggctaatttcataatttgtgtgcagGTTGCTAAAGAAAGTGCAGATGTCATAATTCTGGATGATAATTTCTCCACAATAGTGACAGTGGCCAAATGGGGACGTTCAGTTTACATAAATATTCAAA

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA01G40130.1 (Glycine max), 3'ss of exon 4
-tagatacc-catgaccatgagtaacaatcaattacatgatatctcgagttatttgctatttactcccattttg-aatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA
 |   | |   |  |  ||  ||  |  |   |      | || |  ||| ||||     ||| |    |  || ||  | | |  | ||  | |  |   |||| || ||||| ||||| || ||||| ||||| ||||| ||||||||||| || || ||||| || |||||||| || || |||||||| || |||||||
gtgagtgcaatactataatatgtttccctttgtgctgctacatttt-agtcatttaactcttaattttctactgcaagctaatttctcaatgtatgttc--agGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACTGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 4
----------------------------------------------tagatacccatgaccatgagtaacaatcaattacatgatat-ctcgagttatttgctatttactcccattttg-aatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA
                                              ||   ||| | |   | ||  |  ||    |    || ||   |  ||| | ||     ||| |    |  || ||  | | |  |||| || |  |   |||| || ||||| ||||| || ||||| ||||| ||||| ||||||||||| || || || || || |||||||| || || |||||||| || |||||||
gtgagtgcaatgctatgcaatgtttccctttgtgaaccattcattctacccaccaaaggaaaagaaaaggaaatgttgtgctgctacattttagtcacttaactcttaattttgtactgcaagctaatttcttaatatatgttc--agGTTGCAAAAGAAAGTGCAGATGTCATAATTCTGGATGATAACTTCTCCACGATAGTAACAGTGGCCAAATGGGGACGTTCGGTTTACATAAATATTCAGA

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 4
tagatacccatgaccatgagtaacaatcaattacatgatatc-tcgagttatttgctatttactcccattttgaatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA
                   || |  ||  || | | ||| |  |   || |||||  |         | | | ||  |  || | |   ||   |||  ||||||| |||||||| ||||| ||||||||||| || || ||||||  ||| || ||||| ||||| |||||||| || || |||||||| ||||| ||||
-------------------gtgagtat--atgataagattttgttatgtcatttgtgagagctaaagaatctaaaagtttctatctg-tataaccttttagGTGGCGAAAGAGAGCGCTGATGTCATCATTCTCGACGATAACTTCAGCACGATCGTCACAGTTGCTAAATGGGGACGTTCTGTTTACATAAACATCCAGA

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 4
tagatacccatgaccatgagtaacaatcaattacatgatatctcgagttatt-tgctatttactcccattttgaatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA
                |||||| ||   |   | || |  |||   |||||| ||| |   ||||  |  ||         | |||||     ||||  |||| || ||||||| ||| || ||||||||||| || || ||||||  |||||| ||||| || || |||||||| || || |||||||| ||||||||||
---------------gtgagtatcatatatccaaataa-gtctaatgttattatgcaaacgactcaaacatt---------tttttaa---actcttttagGTAGCGAAAGAGATTGCGGATGTCATCATTCTCGACGATAACTTCAGCACAATCGTCACCGTAGCGAAATGGGGACGTTCTGTTTACATTAACATTCAGA

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0129g00110.t01 (Vitis vinifera), 3'ss of exon 3
tagatacccatgaccatgagtaacaatcaattacatgatatctcgagttattt-gctatttac--tcccattttgaatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA
|| | |  |||  |       ||    ||| | |    | | |  | ||  |    | |  ||  | |||  ||  | || | |||    ||||  ||| | |||||| |||||||||||||| || || ||  | ||||| || |||||||||||||  ||||| || |||||||| || ||||| ||||| || ||||| |
taaa-agtcattgcttgatacaatctacaaattctcattgtttgcacttcctccattgtgaacagtaccaaattctaattaattctgcc-catgaacttca-gGTGGCTAAAGAGAGTGCTGATGTAATAATCTTGGATGATAATTTCTCCACAATTGCGACTGTGGCCAAATGGGGACGTTCAGTCTACATAAATATTCAAA

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv18s0001g09150.t01 (Vitis vinifera), 3'ss of exon 4
tagatacccatgaccatgagtaacaatcaattacatgatatctcgagttatttgctatttactcccattttgaatttgactctttaaca--tgttcttaa----agGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA
       ||||   |  |  |   | |   |   | | ||||   | ||      |  ||| |   |    ||||   |  ||  || |  | |||  ||    ||||||| |||||||||||||| ||||| ||| | ||||| ||||||||||| ||||| ||||| |  |||||||| || ||| |||| || ||||||||||
------tccatcctctgggcttgtagtttgtgtaaagttatcatcactttgaattttattagttttaagcagaatcatatgctgaaaaacttcttcccaatttcagGTGGCAAAAGAGAGTGCTGATGTCATAATTATGGATGATAACTTCTCCACTATTGTGACTGTGGGCAAATGGGGACGCTCAATTTATATTAACATTCAGA

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 4
tagatacccatgaccatgagtaacaatcaattacatgatatctcgagttatttgctatttactcccatt-ttgaatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA
|| |||    | |      |  |||||| |  |  |   ||     |   ||      ||     || |    ||||  | |  |   ||||  ||| | |||||| |||||||||||||| || || ||  | ||||| || |||||||||||||  ||||| || |||||||| || ||||| ||||| || ||||| |
taaataaaagtcattgcttgatacaatctacaaattctcattgtttgcacttcctccattgtgaacagtaccaaattctaattctgcccatgaacttca-gGTGGCTAAAGAGAGTGCTGATGTAATAATCTTGGATGATAATTTCTCCACAATTGCGACTGTGGCCAAATGGGGACGTTCAGTCTACATAAATATTCAAA

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|32923200|gb|CF028012.1|CF028012
EST:     CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAG                         GTGGCCAAAGAGAGTGCTGACGTCATCATCCTTGATGACAACTTCTCCACT
genomic: CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACA
EST: gi|211150741|gb|FL082154.1|FL082154
EST:     CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAG                         GTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACT
genomic: CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACA
EST: gi|33099646|gb|CF059606.1|CF059606
EST:     CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAG                         GTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACT
genomic: CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACA
EST: gi|211150739|gb|FL082152.1|FL082152
EST:     CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAG                         GTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACT
genomic: CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACA
EST: gi|32923223|gb|CF028035.1|CF028035
EST:     CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAG                         GTGGCCAAAGAGAGTGCTGACGTCATCATCCTTGATGACAACTTCTCCACT
genomic: CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACA
EST: gi|32922458|gb|CF027270.1|CF027270
EST:     CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAG                         GTGGCCAAAGAGAGTGCTGACGTCATCATCCTTGATGACAACTTCTCCACT
genomic: CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACA
EST: gi|32923120|gb|CF027932.1|CF027932
EST:     CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAG                         GTGGCCAAAGAGAGTGCTGACGTCATCATCCTTGATGACAACTTCTCCACT
genomic: CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACA
EST: gi|211149318|gb|FL082151.1|FL082151
EST:     CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAG                         GTGGCCMAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACT
genomic: CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACA
EST: gi|211150740|gb|FL082153.1|FL082153
EST:     CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAG                         GTGSCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACT
genomic: CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACA
EST: gi|33099616|gb|CF059576.1|CF059576
EST:     CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAG                         GTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACT
genomic: CTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACA

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: 46 (upstream exon), 49 (downstream exon)
Score: 91

ACTCTACGAAGTTGTGGCTGTGACTGGTGACGGAACAAACGATGCACCTGCTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 193

ACTCTACGAAGTTGTGGCTGTGACTGGTGACGGAACAAACGATGCACCTGCTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 202

ACTCTACGAAGTTGTGGCTGTGACTGGTGACGGAACAAACGATGCACCTGCTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 113

ACTCTACGAAGTTGTGGCTGTGACTGGTGACGGAACAAACGATGCACCTGCTCTTCATGAGGCTGATATTGGGCTTGCAATGGGCATTGCTGGAACCGAGgtaatttcga ... gttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttatttgctatttactcccattttgaatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA
                                    ctttaac  putative branch site (score: 113)
                                            tgttctt  CT-rich tract
                     attttgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagatacccatgaccatgagtaacaatcaattacatgatatctcgagttatttgctatttactcccattttgaatttgactctttaacatgttcttaaagGTGGCCAAAGAGAGTGCTGACGTCATCATTCTTGATGACAACTTCTCCACAATTGTCACTGTTGCAAAATGGGGTCGATCAGTTTACATCAACATTCAGA

- - - -ccatgac
- - - - - - - - - - - - - - - ttacatg
- - - - - - - - - - - - - - - - - - - - - - - - - tttgcta