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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatttgattgttcatttcaatatgaacatttgccttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT

Basic information

species Zea mays
transcript GRMZM2G057576_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 16
-----------------------gttagtatttgattgtt-catttcaatat-gaacatttgc--cttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT
                        |  |  ||| |   || |||| | || | |  || | ||  |||  ||||  || ||| |    | |||| |   ||||| ||| ||||  ||||||||||||||||||||||| || ||||||||||||||||| |||||||| ||||| ||||||||||||||||||||||| || |||||| |||||||||| |
gttagcagttttttcccaataagttcggccttttacctttgcattgccatgttgctcagtggcttcttttacctttatactgttgtgttgctcagtagtttctgtttgaattga-ttgtagGTTTTGGAGATCAACTTGGTCACTTACCCAAATGTTGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 16
----------------------gttag--tatttgattgttcatttcaatat-gaacatttgc--cttagacctgcatgctgctt------aactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT
                      |||||    ||||  | | |||| | || | |  || | ||  |||  ||||  || ||| |          | |||| |   ||||| ||| ||||  ||||||||||||||||||||||| || ||||||||||||||||| |||||||| ||||| ||||||||||||||||||||||| || |||||| |||||||||| |
gttagcagttttttcccaataagttaggccttttgcctttgcattgccatgttgctcagtggcttcttttacctttatactgttgtgtttgtgttgctcagtagtttctgtttgaattgg-ttgtagGTTTTGGAGATCAACTTGGTCACTTACCCAAATGTTGCTGATGCCATCCTTGCTAATGGTATGTTCAGTCATTATGATCGCCCTCGTGTTGCTCAGCTTT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 14
-----gttagtatttgattgttcatttcaat--atgaac--atttgccttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT
      ||| | | |      | || || ||  |||| |  ||| |  ||| |      || |  ||   |    | | | ||     |  | | | || |||||  |||| || ||  | ||||| |  ||||||||||| ||||| ||  | || ||||| ||||| ||||||||||||||||| || ||||||||||| |
gttctcttactttctttgctgtaatctctatccatgagccaattggtgttatatagttttgtt--ttgtttttatatttttttaaatatttactatttt-tagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 16
gttagtatttgattgttcatttcaatatgaacatttgccttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT
       ||   || ||   ||   | | | |  |  || |  | |    || || |  |    |   | | |  |  ||  | | | || |||||  |||| || ||  | ||||| |  ||||||||||| ||||| ||  | || ||||| ||||| ||||||||||||||||| || ||||||||||| |
------gttcttttattttctttgctttaatctgtatccatgaaacaat-tggtgttatatagttttttttttaatattt--actatttt-tagGTACTGGAAATTAATCTTGTGACCTTTCCAAATGTTGCTGATGCTATATTGGCCAATGGCATGTTTAGTCATTATGACCGTCCACGGATTGCTCAGCTTT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 16
--gttagtatttgattgttcatttcaatatgaacatt-tgccttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT
  ||  |   ||  ||  ||||  |  ||||  |||| | |  |  |  | | | ||  | ||||  | |   ||||     || ||||   |  |||| |||||||| ||  | ||||||| ||| |||||||| ||||| ||  | || ||||| |||||||| ||||||||||||||||||||||| ||||| |
gtgtgtggcctttgtttctcatc-cgttatgggcattctactctgaaaattctttct-ttgaactg-ttacgatctt----gtgaattgctgttcagGTGTTGGAGATAAATCTGGTGACTTTCCCCAATGTTGCTGATGCAATATTGGCTAATGGCATGTTCAGCCATTATGACCGTCCTCGTATTGCCCAGCTTT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 16
gttagtatttgattgttcatttcaatatgaacatttgccttagacctgcatgctgcttaactact-caatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT
||  |   ||  ||  |||| |   ||||  |||||  ||  ||      |     | || |  | | ||||        || ||     |  |||| |||||||| ||  | ||||||| ||| |||||||| ||||| ||  | || ||||| |||||||| ||||||||||||||||||||||| || || |
gtgtggcctttgtttctcatct-gttatgggcattttactctgaaaattctttctttgaagtgttacgatgtt------gtgaatcactgttcagGTGTTGGAGATAAATCTGGTGACTTTCCCCAATGTTGCTGATGCAATATTGGCTAATGGCATGTTCAGCCATTATGACCGTCCTCGTATTGCCCAACTTT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 16
gttagtatttgattgttcatttcaatatgaacatttgccttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT
|||   |   | |    | ||| | |       | ||   |   ||| |   |  |||   | || |    ||| |  |    |        |||||||||||||||| || || || |  || ||||| || ||||| ||  | || ||||| |||||||| ||||||||||| |||||| |||||||||| |
gttgaaaagagttgccaccttttacttc-----tctgtgctttccctactcac--cttcctttcttag-accttttagtgcactctcaacacagGTTTTGGAGATCAATTTGGTAACCTTTCCTAATGTGGCTGATGCAATCTTAGCAAATGGGATGTTCAGCCATTATGACCGGCCTCGTGTTGCTCAGCTTT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 16
gttagtatttgattgttcatttcaatatgaacatttgccttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT
        |  ||| ||  || | | |||||  |||   |     ||  |    | |   || |  |||   |||||||    |        |||||||||| |||||  | || || |  |||||||| |||||||| ||  | || ||||||||||| ||||| ||||| || || |||||||| |||||||
---gtcgatctatttttttttcctaaatgaatttttatatagtttcttta----gttctgcttcctaataa-ttctgctctattc-------agGTTTTGGAAATCAATCTGGTTACATTTCCAAATGTCGCAGATGCTATATTAGCTAATGGTATGTTTAGTCACTATGATCGCCCACGTATTGCACAGCTCT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 16
gttagtatttgattgttcatttcaatatgaacatttgccttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT
        ||  || ||   |   ||   |   |||   ||     | |||  |  ||   |  ||| | ||     | |   |||| ||  ||||  |||| |||||  | || ||||||||||||||||||||||| ||  | || ||||| ||||| || |||||||| ||||| || ||||| ||||| |
-------gttacttttttcctctgatgcaat--tttattttcactattcatcattttt---ttttcagt-tccataacatttcttgttttacagGTCCTGGAAATCAATCTGGTAACTTACCCAAATGTTGCAGATGCTATATTAGCAAATGGGATGTTTAGCCATTATGATCGTCCACGGATTGCCCAGCTTT

upper sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 14
lower sequence: PP1S270_53V6.1 (Physcomitrella patens), 3'ss of exon 16
gttagtatttgattgttcatttcaatatgaacatttgccttagacctgcatg-ctgcttaact-actcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT
|| |  |||| |   |  |  |    |   ||||||||  |     |  |||  | ||||||| |  |  |   |||  | || ||        ||| | | || |||||  | || ||||  ||||| || |||||||| ||| |  | ||||| || ||||  ||||||||||||||||| ||||||||||| |
gtaaaaatttaa--atctagcttctcagttacatttgc--tgattttttatgattccttaactcatgctgtactttccacgtgtat------acagGCTCTCGAAATCAATCTTGTCACTTTTCCAAACGTCGCAGATGCGATTTTGACTAATGGCATCTTCAAACATTATGACCGTCCTCGAATTGCTCAGCTTT

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), 45 (downstream exon)
Score: 223

AGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAGgttagtattt ... tgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 154

AGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAGgttagtattt ... tgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 117

AGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAGgttagtattt ... tgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 285

AGAAATATGATACGGGAGGCTACAGCTTTTCTGCTGGATGTTCTGAAGCCAAACTTGCCGGATCATGCTTTTCTTCAAACCAAGgttagtattt ... tgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT
               gcttaac  putative branch site (score: 285)
                                            ttgtctt  putative PPT
                 ttaacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtatttgattgttcatttcaatatgaacatttgccttagacctgcatgctgcttaactactcaatgtcttctgcttggattgtcttgtagGTTTTGGAGATCAACTTAGTGACTTACCCAAATGTTGCAGATGCCATTCTTGCGAATGGTATGTTCAGTCATTATGACCGTCCTCGTATTGCTCAGCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC