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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtatctaattctggatatatatattttctcatgaatggaagttgaacatttagaagggacagtgtcagtagtatattttgtttcataaacatactcgcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG

Basic information

species Zea mays
transcript GRMZM2G164562_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------------gtaagtatctaattctggat----atatatattttctcatgaatggaagttgaacat--ttagaa---gggacagtgtcagtagtatattttgtttc---ataaacatactcgcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG
                                                              |   | |   |  | ||    | | | | || | || || |   || | || ||  ||| |    ||||||| |  ||||  |||||     |    |||| |||| ||  | | ||||||||||||||||||| ||||||| |||||||| || |||||||||||||| ||||||||||| || || |||||||| ||||||
gtaagtacctaagttttttcgcattaatgtattgaaatactacctccgtcccaaaatataacaacttttggctacgaatctggacacacaattgccca-gattcatagctaaaaatgcttatattttgggacagagggagtaacatattaaagctggaaataaccatattcattcccacagGATTACAGTGAAATGGCTAAGGCCTACAGACCTTCACATGCAGATGCAACTTATGACTTCAAATACGGTGTTAGAGCAGTGCAG

upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT1G48850.3 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------gtaagtat-ctaattctggatatatatattttctca---tgaat--ggaagttgaacatttagaaggg-acagtgtcagtagtatattttgtttcataaacatactcgcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG
                            ||| | | ||   | | | ||  || | |||  |    || ||  | |||   |   ||| ||||   | |  | | ||||  | |    ||| |  |||  ||| | || | ||||||||||||||||||||    || || |||||||| ||||| |||||||| |||||| | |||||||| || ||| | ||||||
gtaagttttttttacttctctatgcatataactgtactcgatattgttaactagacttttgctatttgcattagaaagacaacagttttgaagtatagaaagcctgtagattctaacctttgaggaactcactggatttt-cagGATTACAGTGAAATGTCGGTTGCCTATAGACCATCGCATGCTGATGCAACTTATGACATGAAGTATGGTGTCAGATCAGTGCAG

upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtatctaattctggatatatatattttctcatgaatggaagttgaacatttagaagggacagtgtcagtagtatattttgtttcataaacatactcgcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG
     | |    | || |   | |  ||||  |    ||    | |||    || ||    |  | |||   ||| | ||        ||     || | |  | | |||||||| |  |||||||| || ||||| || || || ||||||||||| || ||||||||||||||||| || ||  | ||||||
----ctcttgtttccttgggctttgaatttagtttgtaac--catttgtctcttcagttatg-taatgtt--tagaagatcccaaca-atttttttattggaattttcagGATTATACAGAAATGTCCAAAGCGTATAGGCCTTCACATGCAGATGCTACTTATGACTTCAAGTATGGTGTGAGGTCGGTGCAG

upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0004g02960.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtatctaattctggatatatatattttctcatgaatggaagttgaacatttagaagggacagtgtcagtagtatattttgtttcataaacatactcgcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG
||||||||||   |||   | | | | | |     |   |  |   |  | || || |  | |  |||    || |  || |||       |   || |   ||   |||||||| || ||  |||| | ||| ||||| || || |||||||||||||||||||| ||||||||||| || |||||  | |||
gtaagtatctctctctctctctctctctctctctctctctata---tatatatatatatagtatggtgct--taat-catattgaagagctatgttaatgaatttctcagGATTATAGCGAGCTGTCAAGGGCTTACAGGCCTTCTCATGCAGATGCAACCTATGATTTCAAGTATGGTGTAAGAGCAATCCAG

upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ22409 (Selaginella moellendorffii), 3'ss of exon 3
gtaagtatctaattctggatatatatattttctcatgaatggaagttgaacatttagaagggacagtgtcagtagtatattttgtttcataaacatactcgcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG
                         ||  || || | ||||||||   |||| |     || ||        || | |    |||||               |||| |||||||||   || ||| ||   || ||  | ||||| ||||||||||| || || ||||||||||||||| || ||||||| |||
------------------------gtaagttttcgttaatggaag--aaacact-----ggaact-------taatgtgcggtgttt---------------ttctgcagGATTACTCAGAGATGGCTCTAGCTTATCGGCCATCTCATGCAGATGCTACTTACGACTTCAAGTATGGAATTCGAGCTGTCCAG

upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ25489 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtatctaattctggatatatatattttctcatgaatggaagttgaacatttagaagggacagtgtcagtagtatattttgtttcataaacatactcgcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG
                         ||  || || | ||||||||   |||| |     ||  |        || | |    |||||               |||| |||||||||   || ||| ||   || ||  | ||||| ||||||||||| || || ||||||||||||||| || ||||||| |||
------------------------gtaagttttcgttaatggaag--aaacact-----ggagct-------taatgtgcggtgttt---------------ttctgcagGATTACTCAGAGATGGCTCTAGCTTATCGGCCATCTCATGCAGATGCTACTTACGACTTCAAGTATGGAATTCGAGCTGTCCAG

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|149088514|gb|EE177624.2|EE177624
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|28361588|gb|CB239944.1|CB239944
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|211165635|gb|FL126854.1|FL126854
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGAC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGAC
EST: gi|149070137|gb|EE158538.2|EE158538
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|211165641|gb|FL126860.1|FL126860
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|211165634|gb|FL126853.1|FL126853
EST:     CTGGTAMAC-AATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAG
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAG
EST: gi|211062099|gb|FL126842.1|FL126842
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCANAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAG
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAG
EST: gi|76020355|gb|DT947525.1|DT947525
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCCATCCCATGCAGATGCAAC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACC-ATCCCATGCAGATGCAAC
EST: gi|211165637|gb|FL126856.1|FL126856
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|149015775|gb|EE045474.2|EE045474
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|71442663|gb|DR823713.1|DR823713
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|148963945|gb|EE015067.2|EE015067
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|211062101|gb|FL126844.1|FL126844
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATTCCATGCAGATGCAAC-
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|28390366|gb|CB250180.1|CB250180
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|60352524|gb|DN219497.1|DN219497
EST:     TTGTCCCAAACACAGATCAAGGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: TTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|78089034|gb|DV517427.1|DV517427
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|149100015|gb|EE186068.2|EE186068
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
EST: gi|148966882|gb|EE018003.2|EE018003
EST:     CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGT                         GATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC
genomic: CTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACC

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: 48 (upstream exon), 49 (downstream exon)
Score: 155

GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 430

GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 389

GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 481

GGATGACTACTGGTACACCAATTCACGTCTTTGTCCCAAACACAGATCAAAGGGGTGGTgtaagtatct ... gcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaagggacagtgtcagtagtatattttgtttcataaacatactcgcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG
                                          ctcgcttct  CT-rich tract
                    tatattttgtttcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtatctaattctggatatatatattttctcatgaatggaagttgaacatttagaagggacagtgtcagtagtatattttgtttcataaacatactcgcttctacagGATTACAGTGAAATGTCTAAGGCGTACAGACCATCCCATGCAGATGCAACCTATGACTTCAAGTATGGAGTTAGAGCTGTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT