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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatactctcttctcttccattgatgctatgagctcttatcttatataatctataatctgagctagatctttttccacattcctcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGA

Basic information

species Zea mays
transcript GRMZM2G053764_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------------------gtgagatactctcttctcttccattgatgctatgagctcttatcttatataatctataatctg------agctagatctttttccacattcctcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGA
                                            |  | |    |  | |||| ||  ||||   || |  |  ||| | | |||  |  ||||      |  | ||| | ||||    ||  |  ||  ||||| | |||||||| |||||||| || ||||| || ||  | || || || || || || |||||||| ||||| ||||||||||| ||||||||||| ||
gtaagataatgtcctacaatatttctttttccgtggcttctactaacttcaaagtcatgttccttt--tgctcatagattcttccttgttttatcagttgtctgcttaagaagttgatatctttcttttttatttattaacagATTTGGTAAATGTGTTTGAAGTGTTTCTTCCTCAACTTCTTCTCTACCCCAACCCATCAGATCCATTGAATGGAGAGGCTGCAGCCCTGATGATGCGAGA

upper sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------gtgagatactctcttctcttccattgatgctatgagctcttatcttatataatctataatctgagctag----atctttt-tccacattcctcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGA
                                         |  ||    | | ||  |||  | ||    |        ||  || ||   |  ||  | |||||||     ||| | | |  |||    | |||| ||||||| ||||| || ||||| || |||||||| || ||  |  | ||||| || || || |||||||||||||| ||||||||||| || |||||||||||
gtaatgattaacaaactcatttggcattcttgttcgataaataggacttccgcatcgtttctctggagaaaaaacaaagctactttttagttttaatggtttgagctactgttatcgtatgttgacacctgtgttttccagATCTGGTAAACGTGTTTGAGGTGTTCCTTCCGCAACTTCTTTTGTATCCCAACCCATCAGATCCATTAAATGGAGAGGCTGCAGCTCTAATGATGCGTGA
















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|12968800|gb|BG265836.1|BG265836
EST:     TGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|5895766|gb|AW037012.1|AW037012
EST:     TGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|6022600|gb|AW067412.1|AW067412
EST:     TGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|5713918|gb|AI943903.1|AI943903
EST:     GGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGNAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: GGCTCTGTATGTTTAGATGTCATAAACCAAACATGG-AGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|5895785|gb|AW037031.1|AW037031
EST:     TGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|60396538|gb|DN229407.1|DN229407
EST:     TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|60355446|gb|DN222419.1|DN222419
EST:     TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|5649980|gb|AI920340.1|AI920340
EST:     TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|1337735|gb|W49441.1|W49441
EST:     TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|71328419|gb|DR800850.1|DR800850
EST:     TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|5608383|gb|AI901960.1|AI901960
EST:     TGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|87156694|gb|DY401483.1|DY401483
EST:     TGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|5895786|gb|AW037032.1|AW037032
EST:     TGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|5917370|gb|AW054161.1|AW054161
EST:     TGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|22715330|gb|BU197707.1|BU197707
EST:     TGGCTCTGTCTGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA
EST: gi|211363205|gb|FL271919.1|FL271919
EST:     TGGCTCTGTATGTTTANATGTCATAAACCAAACATGGAGCCCAATGTTTG                         ATCTAGTAAATGGTTTTGAAGNATTCCTTCCACAGCTGTTACTATATCCAA
genomic: TGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAA

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), 49 (downstream exon)
Score: 654

GTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1373

GTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1247

GTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 916

GTCTGGCTCTGTATGTTTAGATGTCATAAACCAAACATGGAGCCCAATGTTTGgtgagatact ... tcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttatataatctataatctgagctagatctttttccacattcctcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGA
                             tctttttccacattcc  CT-rich tract
     atataatctataatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatactctcttctcttccattgatgctatgagctcttatcttatataatctataatctgagctagatctttttccacattcctcttttgcagATCTAGTAAATGTTTTTGAAGTATTCCTTCCACAGCTGTTACTATATCCAAATCCTTCTGATCCATTAAATGGGGAGGCTGCAGCACTGATGATGCGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG