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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtctatttcaccaaattgtttgttgtttactaaagtttggttttggaacactgtaaatatttctttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG

Basic information

species Zea mays
transcript GRMZM2G075978_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 3'ss of exon 10
gtaggtctat-ttcaccaaattgtttgttgt--ttact-aaagtttggttttggaacactgtaaatatttctttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG
||| |  | | ||| |   |  | || ||||  ||||| ||||||  ||||   |  |||  ||   ||  |||  || ||||||| |||||||||||||||||||| |||||||||||||||||||||||||| |||||||| ||||| |||||||| ||||| ||||| ||| |
gtaagcttgtcttccctgcaaggattattgtgtttactcaaagttctgtttcctagaactaaaagacttattttccctgtacagCGAGAGTTTTATTTGGAAGGAGGGGCCATGGTTTTGGCTGATGGTGGAGTTGTTTGTATTGATGAGTTTGACAAAATGAGGCCTGAGGACCG

upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------gtaggtctatttca--ccaaattgtttg-ttgtttactaaagtttggttttggaacactgtaa---atatttctttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG
                                                   ||   ||  || |     |||  |  | |||    | |    ||   |||  ||  || | |   || ||   |  |||||  |||||||||||||| | |||||||| || ||||| ||||| ||||| || || || || || || || ||||| |||||||| || ||||||||
gtaagttcttaccttcctaaactgtttgtattagatcgcaaatttctactatactacttgttgaggtataatcataagcttgacctccatcaattttctttacaagtctctgattcatgttctatggtctctttagCGTGAGTTTTATCTTGAAGGAGGGGCTATGGTCTTGGCCGATGGAGGTGTTGTCTGCATTGACGAGTTTGATAAGATGAGGCCAGAAGACAG

upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT2G07690.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaggtc-tat-ttcaccaaattgtttgttgtttactaaagtttggtt-ttggaaca---ctgtaaatatttct-----ttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG
||| ||| ||| ||||     || | | |  |||  | ||   | |||  |   |||       |  ||||| |     | |||  | ||||| ||||| ||| | ||||| || || ||||||||||||||||| || || || ||||| ||||||||||||||||||||||| ||||| ||
gtatgtcctatcttcaagtgtttttctatgatttgtttaaaagtagttgctatgacagattctcagttatttatacatatgttcattgcagCGAGAGTTCTATCTTGAAGGTGGTGCTATGGTTTTGGCTGATGGAGGTGTTGTGTGTATTGATGAATTTGACAAGATGAGACCGGAAGATAG

upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 9
-------------------------------------------------------------------------------gtaggtctatttcaccaaattgtttg---ttgtttactaaagtttggttttggaacactgtaaatatttctttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG
                                                                               ||   |  |    |  |  || |||    |   | |  | | || |||| |   ||     |   |     |      | |||||||| |||||| | ||||||||||| ||||||||||| ||||| || || || ||||| ||||| |||||||| |||||  | || |||||
gtaagtttttgagattctctatcatgtgtgctgatcctaatgtcaattctctagctctttctttctccagataagctttgtcaatggagccgatgagtttatttaaattccctcaaaataattaggttatctgacttcaaattcaaactctacatgattcagCGTGAATTTTATCTAGAAGGAGGAGCAATGGTTTTGGCAGATGGAGGTGTTGTCTGTATTGATGAGTTTGACAAAATGAGGGCAGAGGACAG

upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ31205 (Selaginella moellendorffii), 3'ss of exon 10
gtaggtctatttcaccaaattgtttgttgtttactaaagtttggttttggaacactgtaaatatttctttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG
    ||    |||   ||||     | | | |  |  | ||  |||||    || |  |  | | |  | |||    ||||| ||||| ||||| || |||||||| |||||  | || ||||| || || ||||| || || ||||||||||||||||| || ||||||||
----gtaggcttccgtaaat-----gctatctgttccactt--gttttttttcattcaatttgtatgatgttc----cagCGAGAGTTCTATTTAGAGGGAGGAGCGATGGTGCTTGCCGATGGAGGGGTGGTTTGCATTGACGAATTTGACAAGATGAGGCCAGAAGACAG

upper sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ17142 (Selaginella moellendorffii), 3'ss of exon 10
gtaggtctatttcaccaaattgtttgttgtttactaaagtttggttttggaacactgtaaatatttctttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG
    ||    |||   ||||     |   | |  |  |  ||| ||||   |  |       |||| | |     | ||||| ||||| ||||| || |||||||| |||||  | || ||||| || || ||||| || || ||||||||||||||||| || ||||||||
----gtaggcttccgtaaat-----gccatctgttcca-cttgtttttttcattca------atttgtatgatgttccagCGAGAGTTCTATTTAGAGGGAGGAGCGATGGTGCTTGCCGATGGAGGGGTGGTTTGCATTGACGAATTTGACAAGATGAGGCCAGAAGACAG

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: 165

AAAATTTGTAGAGAAGACTGCACCTATTGCAGTATATACATCTGGCAAAGGATCGTCTGCAGCTGGTCTTACAGCATCTGTAACTCGTGATAGTAGCTCGgtaggtctat ... ttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG


Block sizes: 43 (upstream exon), 44 (downstream exon)
Score: 47

AAAATTTGTAGAGAAGACTGCACCTATTGCAGTATATACATCTGGCAAAGGATCGTCTGCAGCTGGTCTTACAGCATCTGTAACTCGTGATAGTAGCTCGgtaggtctat ... ttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 15

AAAATTTGTAGAGAAGACTGCACCTATTGCAGTATATACATCTGGCAAAGGATCGTCTGCAGCTGGTCTTACAGCATCTGTAACTCGTGATAGTAGCTCGgtaggtctat ... ttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG


Block sizes: 44 (upstream exon), 43 (downstream exon)
Score: 9

AAAATTTGTAGAGAAGACTGCACCTATTGCAGTATATACATCTGGCAAAGGATCGTCTGCAGCTGGTCTTACAGCATCTGTAACTCGTGATAGTAGCTCGgtaggtctat ... ttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtttactaaagtttggttttggaacactgtaaatatttctttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG
      tactaaa  putative branch site (score: 9)
                                    tatttctttttctcta  putative PPT
                              tgtaaatatttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtctatttcaccaaattgtttgttgtttactaaagtttggttttggaacactgtaaatatttctttttctctacagCGTGAGTTTTATTTGGAAGGAGGAGCCATGGTTTTGGCTGATGGTGGAGTAGTTTGTATCGATGAATTTGACAAGATGAGACCTGAAGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA