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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcataattgatttcttttcttctccagattttgaagaaaatattcctttttcaaaattttctaataacagttgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG

Basic information

species Zea mays
transcript GRMZM2G124886_T04
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 18
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 9
gcataattgatttcttttcttctccagattttgaagaaaatattc--ctttttcaaaattttctaataacagttgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG
||| |  |||||  |||  || || | ||||  |||||  | ||   |||| |  |||| || | | |  | ||||||| ||||  ||||| | |||||  |||||||| |||||||||| ||| ||||| ||||||||||||||||  ||||||
gcacagatgattaatttatttatc-acatttccaagaatgtttttgtctttgttcaaatgttgtta-actatttgcttttcagGCAATTGCCATTGAGGCACAAAGTGAGTCCAAGTGGAGGCAGTTAGGAGAGTTAGCTATGTCAACCGGAAAG

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 18
-----------------------------------------------------gcataattgatttcttttcttc--tccagattttgaagaaaatattcctttttcaaaattttc----taataacagttgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG
                                                      ||    |  ||  |||||| |  | |  ||||  | ||   |  |     || | | | |      |  | |  |||  ||||||||  ||||| ||||| ||||| ||||| ||||| ||||||||||| || || ||||| ||||| | |||||||
gtaagttcatatgttcctgcaaggatatattattttacttgtgaaatttaataacactgctatttaattttctgcatttctaatttgcacgagtttgatttgagtttatattgtgagcaatgttcattgttcttttgcagGGTATTGCCACTGAAGTGCATAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 18
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 7
------------------------------------------------gcataattgatttcttttcttctccagattttgaag--aaaatattcctttttcaaaattttctaataacagt--------tgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG
                                                 ||||| |    | |||  || ||   ||||  ||     | || |    ||| |   | |  |   |  | |        |  ||||||||  |||||| |||| ||||| ||||| ||||| ||||||||||| || || ||||| ||||| | |||||||
gtaagttcatatgttcctgcaaggatatattatttgactcgtgaaatttcataactctgctatttaattttctgcatttctaatttgcactagtttgatttgagtttatattgtgagtaatgctcatcttcttttgcagGGTATTGCTTCTGAAGTGCAGAGTGAGTCCAAATGGAAGCAATTGGGAGAATTAGCCATGTCTACTGGAAAG

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 18
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 18
---gcataat---tgatttcttttcttctccagattttgaagaaaatattcctttttcaaaattttctaataacagttgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG
     |||||   ||||  ||    | ||    |  ||   | | |    |  | || |||  | | |  |||    ||| | | |||  || |||   || || || || ||||| |||||||| |||||||| ||||||||||||||    ||||||
gtgatataatgtgtgatgactaagatactttttaacttcttgtatagtggcaatatttaaacatgttttttaatttatgcct-gtagGAAATCGCTGTGGAAGTACAGAGCGAATCTAAGTGGAAACAATTAGGAGAGTTAGCTATGTCCTCCGGAAAG

upper sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 18
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 18
-----------------------------------------------------------------gcataattgatttcttttcttctccagattttgaagaaaatattcctttttcaaaattttct---------aataacagttgctttgc----agGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG
                                                                 | | | || |   | | | |  |      |  | |   | || |||| | | | |||||| |         |  |  |  | ||||||    |||  |||||||| || ||||||||||| || || ||||||||||| || || ||||||||||| | |||||||
gtaaattatgttgattttatgtcagtatagggatataaactagttctttgacagtttgttgacttgaacatttaagcacatctttattttcttctgaggaatgattagtcctctgtgacaattttatctgaaatatagcatgatcttctttgctttcagGACATTGCTACAGAAGTGCAAAGTGAGTCAAAATGGAAGCAATTGGGAGAATTAGCTATGTCCACTGGAAAG

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|33093602|gb|CF053596.1|CF053596
EST:     ATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGACTTGAAATAGCGAAG                         GTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGACTTGAAATAGCGAAGgcataattga ... tgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAG
EST: gi|111145650|gb|EE257974.1|EE257974
EST:     ATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGACTTGAAATAGCGAAG                         GTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGACTTGAAATAGCGAAGgcataattga ... tgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAG
EST: gi|32929286|gb|CF034098.1|CF034098
EST:     ATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGACTTGAAATAGCGAAG                         GTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGACTTGAAATAGCGAAGgcataattga ... tgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAG
EST: gi|60337834|gb|DN204807.1|DN204807
EST:     ATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGACTTGAAATAGCGAAG                         GTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAG
genomic: ATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGACTTGAAATAGCGAAGgcataattga ... tgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAG

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: 230

GGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGACTTGAAATAGCGAAGgcataattga ... tgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

GGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGACTTGAAATAGCGAAGgcataattga ... tgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 280

GGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGACTTGAAATAGCGAAGgcataattga ... tgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 390

GGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGACTTGAAATAGCGAAGgcataattga ... tgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttgaagaaaatattcctttttcaaaattttctaataacagttgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG
                                   taataac  putative branch site (score: 390)
                                            ttgcttt  putative PPT
       aagaaaatattccttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcataattgatttcttttcttctccagattttgaagaaaatattcctttttcaaaattttctaataacagttgctttgcagGTGATTGCTACTGAGGTGCAAAGTGAATCCAAGTGGAAGCAATTAGGGGAGTTAGCTATGTCAAATGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA