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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgacttccaaacacgattttgttagctatgttcttaacttcttgtttcaatgttgatttgtaattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG

Basic information

species Zea mays
transcript GRMZM2G052880_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g25580.2 (Oryza sativa), 3'ss of exon 8
actgacttccaaacacgattttgttagctatgttcttaacttcttgtttcaatgttgatttgtaattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG
| | | ||  | |      ||   | ||     ||     |  ||||     | |||| || | |||   || |       |||   ||    | | |||||| |  |||||  |||| |  |||||||| |||||||||||||| ||||||||||||||||| ||||||||||| |||||||| || |||||||||
atttatttggacatgtatgttgagttgcatgagtccattttgtttgtaatgttcttgacttattattttaatggtcattgcttcatgtttaaattaccagAACTGGGGGAGAGATATCCAATAGAGATTTGCAAAAAATGGTTCAAGCTCTTCCACAGTACAGCGATCAAATTGAGAAGCTTTCTCTTCATGTTGAG

upper sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA01G42140.1 (Glycine max), 3'ss of exon 8
---actgacttccaaacacgat-tttgttagctatgttcttaacttcttgtttcaatgttgat--ttgtaattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG
   |   |   | | |     | |||| | |   ||||  |   || ||  |  | |  |  |  |   ||     | | |||| ||||   | | |||  |  || | |  |   ||| | || ||||| ||  ||||||  || ||||| || ||||||||||||||||| |||||||||||||| ||||| ||||| |||
tttagctaagcctagatttattgtttgatggaagtgtttct---ttattaatctagttctcgtcataacaaacttaaattattgaattttgttgtatttatagTAGTAGCAGT---GAAATGTCTACAAGGGACATACAAACCATCGTTCAAGCACTTCCACAGTACAGTGAACAAATTGATAAGCTCTCCCTCCATGTAGAG

upper sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA11G03230.1 (Glycine max), 3'ss of exon 12
actgactt--ccaaacacgattttgttagctatgttcttaacttcttgtttcaatgttgatttg-taattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG
  |  ||   || |     ||| | | |   | ||| | |  |  |  | |   | | |   |   ||     | | |||| ||||   | | |||     ||||      | ||| | || ||||| ||  ||||||| |||||||| || ||||||||||||||||| |||||||| ||||| ||||| ||||| |||
tttagctaagcctagatttattgtttgatggaagttttgatttattcatctagttctcgtcataacaaacttaaattattgaattttgttgtatttat---agAAGTAGCAGTGAAATGTCAACAAGGGACATACAAAAGATGGTTCAAGCACTTCCACAGTACAGTGAACAAATTGACAAGCTCTCCCTCCATGTAGAG

upper sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT1G12360.1 (Arabidopsis thaliana), 3'ss of exon 12
actgacttccaaacacgattttgttagctatgttcttaacttc-ttgtttcaat-gttgatttgtaattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG
 || || |      ||| |  | |  |   | | ||| | ||  ||     | | | |  | | |  ||  |||  |||   |||  || | ||||| | |||   |  |  ||  | || ||||||||||| || || |||||||| ||  | |||||||||||||| |||||||| ||||| || || || || |||
-cttacattactctacgttgatctatgtggtatactttatttggttagagaagtaggtcttctctccttttgatcaattttgtttgactcttttttc-ttagAGATGGAGCTGAGCTTTCTACAAGAGATTTGCAGAAGATGGTTCAAGCATTGCCACAGTACAGTGAACAAATTGACAAGCTCTCTCTCCACGTAGAG

upper sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv13s0019g05000.t01 (Vitis vinifera), 3'ss of exon 12
actgacttccaaacacgattttgttagctatgttcttaacttcttgtttcaatgttgatttgtaatt-aggattgattgcatt---tccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG
       ||        || | ||||    |  |  |   | |  || |  ||   ||   |||||  |||||   ||    |   |   | ||| ||    |||   | ||| ||||| || ||||| || || ||||| |||||||| ||| | ||||| || ||||| |||||||| ||||||||||| |||||||||
--atgtatctttgtgatatctggttaatctttctacttgatgccagtgt--attcagaccagtaatccaggatgtgttaacctaaatatttatctgttatgtagAGGTGGTGGTGAATTGTCTACAAGGGACTTGCAAAAGATGGTTCAAGCTTTGCCACAATATAGTGAGCAAATTGAGAAGCTTTCCCTCCATGTTGAG

upper sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 12
lower sequence: EFJ13784 (Selaginella moellendorffii), 3'ss of exon 12
actgacttccaaacacgattttgttagctatgttcttaacttcttgtttcaatgttgatttgtaattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG
                                           | || ||  |  |  ||| || ||  ||    ||  |||  | | |   ||   |||    | |  | |  |  | ||||||||| | || ||  | |||||||| |||||||||||| | ||||||||||| |||||   ||| ||  |||| 
------------------------------------------gtagtctctctagttcttt-tatttctga---gttttattaacgtcttcattttccag-

upper sequence: GRMZM2G052880_T01 (Zea mays), 3'ss of exon 12
lower sequence: EFJ29221 (Selaginella moellendorffii), 3'ss of exon 12
actgacttccaaacacgattttgttagctatgttcttaacttcttgtttcaatgttgatttgtaattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG
                                             || ||  |  |  ||| || ||  ||    ||  |||  | | |   ||   |||    | |  | |  |  | ||||||||| | || ||  | |||||||| |||||||||||| | ||||||||||| |||||   ||| ||  |||| 
---------------------------------------------gtctctctagttcttt-tatttctga---gttttattaacgtcttcattttccag-

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|67022604|gb|CO451353.1|CO451353
EST:     CTTCATTTTAAAGAACAAAGCTGCACAATTGCATCAAGCACG                         AACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCT
genomic: CTTCATTTCAAAGAACAAAGCTGCACAATTGCATCAAGCACGgtatattgtt ... ttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCT




















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: 45 (upstream exon), 47 (downstream exon)
Score: 52

GCAAGTGAGAGGCTACATGATAAGATGACCAACTTCATTTCAAAGAACAAAGCTGCACAATTGCATCAAGCACGgtatattgtt ... ttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 126

GCAAGTGAGAGGCTACATGATAAGATGACCAACTTCATTTCAAAGAACAAAGCTGCACAATTGCATCAAGCACGgtatattgtt ... ttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 150

GCAAGTGAGAGGCTACATGATAAGATGACCAACTTCATTTCAAAGAACAAAGCTGCACAATTGCATCAAGCACGgtatattgtt ... ttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 39

GCAAGTGAGAGGCTACATGATAAGATGACCAACTTCATTTCAAAGAACAAAGCTGCACAATTGCATCAAGCACGgtatattgtt ... ttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcaatgttgatttgtaattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG
                        gattgat  putative branch site (score: 39)
                              ttgcatttccctttct  CT-rich tract
         ttgatttgtaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgacttccaaacacgattttgttagctatgttcttaacttcttgtttcaatgttgatttgtaattaggattgattgcatttccctttcttttcatcagAACCGATGGAGAATTATCGACAAGAGATTTACAAAAAATGGTTCAGGCTCTTCCACAGTACAGTGATCAAATTGATAAGCTTTCCCTGCATGTTGAG

- - - - ccaaaca
- - - - - - - - - ttttgtt
- - - - - - - - - - - - - - - - - - - - - - tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - tgttgat