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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacttgatctgttcagataatttgtgaaatgctttcatgcctttccatttgaagtggcaaacaataatctgttgattttaactcatttgttttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG

Basic information

species Zea mays
transcript GRMZM2G036034_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 16
-----tacttgatctgttcagataatttgtgaaatgctttcatgcctttccatttgaagtggcaaacaataatctgttgattttaactcatttg--ttttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG
     |  || ||   || ||   |||  | |      | ||||    | || |||| |  | | ||  |  |    || |||||  | | | |   | |||||||||||||||||||||| |||||| |||| |||||||| ||||||||||||||||||||||||||||| |||||   |||||||||||||||||||||||| |
taatattttttattccttgaggagatt-attatgcatctacatg----ttcagttgatgcagtagacggt--ttgactggttttatttaactggaactgtgtttcagGTTGATCCATCCACAGGTGAAGCTGATGATGATGGCGTTGAGGATGAGTACCAGCTTGAAGATCTGGAAATTACTTCTGCTGATTATATGTTGAAGGTTG

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 16
-------------------------------------------------------------------------------tacttgatctgttcagataatttgtgaaatgctttcatgcctttccatttgaagtggc--aaacaataatctgttgat-----tttaac-------tcatttgttttgttt----cagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG
                                                                               |   |  |     |    |  || |   ||  ||   || |     |||||  |      |||||||||| | ||  |     | |||        |||| | ||   | |    |||||||| ||| |||| ||||| || ||||||||||||||||| ||||| ||||| || || ||| | ||  | ||  | || || || || ||||| ||||
gtacttgtcccctttatccttgggaagcattgtggtttttctttgtcctagtcctagacccctggtatatatcacgaagtgtatatttcaagcgtggagcttattttatttttctctggcacggaatttgtggaaaataaaacaataatatttttgtggaaatctaatcactgcttcatgtattggatattgaccagGTTGACCCAACCACTGGTGAGACAGAAGATGATGGTGTTGAAGATGAATACCAACTGGAGGATTTGGAGGTTGTCACAGCAGACTACATATTGAAAGTGG

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA06G01520.1 (Glycine max), 3'ss of exon 16
---------------------------------------------------------tacttgatctgttcagataattt----gtgaaa--tgctttcatgcctttccatttg--aagtggcaaacaataatctgttg-atttt-------aactcatttgt------------tttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG
                                                         |  ||    |  |   ||||||     |||||   || ||| ||   ||||  || |  || | |   | ||||| || |   |||||       ||||||| | |            | |  |||||||||| ||| |||| |||||  |||||||||||||||| || ||||| |||||||| || ||||| || || ||| | || |||||  ||||||| ||||
gtattatcctctcttttttttttctgaacctttctggttttttattatttcatgtcatgattatgtttatattataattcaagcgtgaagcttgtttttatatttttcatttagggaatttgtggaaaataacctataatatttttgtagcaaactcatctctagattaactggatcttcttcagGTTGACCCAACCACTGGTGAGGCTGAAGATGATGGTGTCGAAGATGAATACCAGCTGGAGGATCTGGAGATTGTTGCAGCAGATTACGTGTTGAAAGTGG

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 15
---------------------------------------------------------------------------------------tact-tgatctgttcagata--atttgtgaaatgctttcatgcctttccatttgaagtggcaaac------aataatctgttgattttaactcatttgttttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG
                                                                                        ||   ||    ||  || |  | |     || |  |  |     |  ||    |    | ||||      | ||   ||||  |  |        ||| ||    |||||||| |||  ||| |||||| | ||||||||||| || || |||||||||||||| || ||||||||  | ||  |||  ||||| ||| |||| ||||
gtacatgttaaataggctattcacttccatctttttatttacttacactgaaaatgaccccataatactttgtggagaactcttataaacaacgactcatttggagaggagtaccagaacgactcaaattaatcacagaaaacaaagaaaactctctaactacattgtttgtgcttttatgaatgtgttaaaacagGTTGACCCAAGCACAGGTGAAGCAGAAGATGATGGAGTAGAAGATGAGTACCAGCTAGAGGATCTTGAGGTTGTAGCTGGAGATTACATGGTGAAAGTGG

upper sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 16
tacttgatctgttcagataat-ttgtgaaatgctttcatgcctttccatttgaagtggcaaacaataatctgt---tgattttaactcatttgttttgttt-------cagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG
           |  | || |   |     |||||| ||| |   |  | |   | |  | ||||| ||  | |   || |||| | |||| ||||||||||       |||||||||||| | || ||||| || || || |||||||| || || || |||||||| || || |||||| | ||| | ||||||||| |||||||||| |
-------caaatagaaattacactagaggatgcttccatactgatgaact---aatctccaacaaaaaattctacatggttttca-tcatgtgttttgtttatatttccagGTTGATCCAACTACTGGTGAGACAGAGGAAGATGGTGTCGAAGACGAATACCAGCTGGAGGACCTTGAAGTTGTTGCAGCTGATTATGTGTTGAAGGTTG

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|31358343|gb|CD442700.1|CD442700
EST:     TCATTGCTACTGGCAAGTTCTCAAATATCCTGAAATTCATTGTTAAGGAG                         GTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTAC
genomic: TCATTGCTACTGGCAAGTTCTCAAATATCCTGAAATTCATTGTTAAGGAGgtatatattt ... tttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTAC
EST: gi|211418625|gb|FK952671.1|FK952671
EST:     TTCATTGTTAAGGAG                         GTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTAC
genomic: TTCATTGTTAAGGAGgtatatattt ... tttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTAC

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: 214

ATATGATTCTCCTGGGCAGACCTTTGTCGCTTTTGAGAAGCCAGAAGGTGTCATTGCTACTGGCAAGTTCTCAAATATCCTGAAATTCATTGTTAAGGAGgtatatattt ... tttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 198

ATATGATTCTCCTGGGCAGACCTTTGTCGCTTTTGAGAAGCCAGAAGGTGTCATTGCTACTGGCAAGTTCTCAAATATCCTGAAATTCATTGTTAAGGAGgtatatattt ... tttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

ATATGATTCTCCTGGGCAGACCTTTGTCGCTTTTGAGAAGCCAGAAGGTGTCATTGCTACTGGCAAGTTCTCAAATATCCTGAAATTCATTGTTAAGGAGgtatatattt ... tttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 221

ATATGATTCTCCTGGGCAGACCTTTGTCGCTTTTGAGAAGCCAGAAGGTGTCATTGCTACTGGCAAGTTCTCAAATATCCTGAAATTCATTGTTAAGGAGgtatatattt ... tttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgaagtggcaaacaataatctgttgattttaactcatttgttttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG
                              ttttaac  putative branch site (score: 221)
                                            ttttgtttc  putative PPT
                             attttaactcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacttgatctgttcagataatttgtgaaatgctttcatgcctttccatttgaagtggcaaacaataatctgttgattttaactcatttgttttgtttcagGTTGATCCATCCACGGGTGAAACTGAAGATGATGGTGTTGAGGATGAGTACCAGCTTGAAGATCTTGAAATAGTTTCTGCTGATTATATGTTGAAGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - tgatctg
- - - - - - - - - - - - tgaaatg
- - - - - - - - - - - - - - - - -ttcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatttg