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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttagatcacgatccattaccacccctaactacagtatataaatgttgttttattgtatatgtttttttttctcatcacgttgtgctgcttgtttattagGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT

Basic information

species Zea mays
transcript GRMZM2G320786_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G320786_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g27700.1 (Oryza sativa), 3'ss of exon 5
tttagatcacgatccattaccacccctaactacagtatataaatgttgttttattgtat-atgtttttttttctcatcacgttgtgctgcttgtttattagGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT
          |||| ||||       ||| | | |  ||||  | ||  | ||  || | |  | || ||||    |    ||    || |  || || |||||||||||| ||||||||||| || |||||||||  ||||||||| ||||||||| |||||||||||||  |||||||||| ||  | ||||| ||| |
------gtgagatcaattattcagattaatttcggattatagctcttcatgtacagttttaaatattctttttgtgtttattttgattgttcattgatcagGTGTGTGGTTCATGCATTGCCATTTTGATCGTCACGTGGTGTGGGGGATGGACACTATGTTCATCGTGAAGGATGGCAAGACGCCGCAGGCTCAGATGCT

upper sequence: GRMZM2G320786_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g30140.1 (Oryza sativa), 3'ss of exon 4
tttagatcacgatccattaccacccctaactacagtatataaatgttgttttattgtatatgtttttttttctcatcacg--ttgtgc---tgcttgtttattagGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT
    |      || |          |  | |   |||| |  || | ||  | |  | |    ||||||||   |  | |  | |||    |  |  ||  | |||||||||||| ||||||||||| || ||||| |||  ||| ||||| |||||||||||||||||||||||  |||||||||| ||  | ||||| ||| |
----gtgagttattcggatttcgatcggattgtggtattttgatatagtactttcatgtgcagttttttttaaaaaaaaggttcgtgtttattttcattgttcagGTGTGTGGTTCATGCATTGCCATTTTGATCGCCACGTGGTATGGGGGATGGACACTGTGTTCATCGTGAAGGATGGCAAGACGCCGCAGGCTCAGATGTT

upper sequence: GRMZM2G320786_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g47390.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------tttagatcacgatccattaccaccccta-actacagtatataaatgttgttttattgtat-atgtttttttttctcatcacgtt-gtgctgcttgtttattagGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT
                                   | |  || | |  | ||||  |  | |  |  | ||  |  |  |   ||||| || | | |  ||    ||| |  ||| |||  |  || ||||| |   ||||||||||| ||||||||||| || ||||| |||| ||||||||| ||| | |||||||||||||||||  |||||||||| ||| | ||||| ||| |
gtaactttttttctgatgattcctcttttggtttctgtgaattatg--ctattattatgcttgtatcaaagagttcatgtccagttttctttttttaaattaaaattttttttcatgtttattttgattgttca---gGTGTGTGGTTCATGCATTGCCATTTTGATCGACACATGGTGTGGGGAATGAATACTGTGTTCATCGTGAAGGATGGCAAGACGCCACAGGCTCAGATGCT

upper sequence: GRMZM2G320786_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g51440.1 (Oryza sativa), 3'ss of exon 4
tttagatcacgatccattaccacccctaactacagtatataaatgttgttttattgtatatgtttttttttctcatcacgttgtgctgcttgtttattagGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT
          ||   |||   |   |  | ||  || | | |   | || ||  |||| | ||||||  |  |  |  |||  |  |  |  ||  | |||||||||||| ||||||||||| || ||||| |||  ||||||||| |||||||||||||||||||||||  | |||||||| ||  | ||||| ||| |
------gtgagagttattcagatttcggattatggtctttgatattggtctttatgtaca-gtttttaatatttttttcgtgtttattttgattgttcagGTGTGTGGTTCATGCATTGCCATTTTGATCGCCACGTGGTGTGGGGGATGGACACTGTGTTCATCGTGAAGGACGGCAAGACACCGCAGGCTCAGATGCT

upper sequence: GRMZM2G320786_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0001g00340.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------tttagatcacgatccattaccacccctaactacagtatataaatgttgttttattgtatatgtttttt--tttctcatcacgttg-tgctgcttgtttatt--agGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT
                               |||  |  |  | || ||   ||  | ||||    || |   |  |  ||||  |  ||||     |   ||     | | |||| |     || | | ||  ||| |||||||| ||||| |||||  | || |||||   |   |||||||||||||||| |||||| ||||||||||| ||   |||| | |||||| || |
gtatgttgcaagcactcatgtgaatttttttttttaaaaaaaaacccttgaaactgccaactcgcatacaaggaaataatttttcttaatattgcaataagttaggtgtaatgttggtatattttctctgttgcagGAGTGTGGTTCATGCACTGCCATGTAGAACGTCATCAGACTTGGGGCATGGACACTGCGTTCATAGTGAAAAATGGTAAACACCCAGAAGCTCAAGTGCT

upper sequence: GRMZM2G320786_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0001g01010.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------tttagatcacgatccattaccacccctaactacagtatataaatgttgttttattgtatatgtttttt--tttctcatcacgttg-tgctgcttgtttatt--agGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT
                                |||   | |  | || ||   ||  | |||     || |   |  |  ||||  |  ||||     |   ||     | | |||| |     || | | ||  ||| |||||||| ||||| |||||  | || || ||   |   |||||||||||||||| |||||| ||||||||||| ||   |||| | |||||| || |
gtatgttgcaagcactcatgtgaattttttatttttttttaaaaacccttgaaactgccaacctgcatacaaggaaataatttttcttaatattgcaataagttaggtgtaatgttggtatattttctctgttgcagGAGTGTGGTTCATGCACTGCCATGTAGAACGCCATCAGACTTGGGGCATGGACACTGCGTTCATAGTGAAAAATGGTAAACACCCAGAAGCTCAAGTGCT

upper sequence: GRMZM2G320786_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0001g00400.t01 (Vitis vinifera), 3'ss of exon 5
---------------------------------tttagatcacgatccatta--ccacc--cctaactacagtatataaatgttgttttattgtatatgtttttttttctcatcacgttgtgctgcttgtttattagGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT
                                 |||| |  |  | || | |  |  ||  |||   ||||    |  ||| ||  || ||  | ||     ||   | | ||   | | |  |   | | |  |||| |||||||| ||||| |||||  | || || ||   |   |||||||||||||||| |||||| ||||||||||| ||   |||| | |||||| || |
gtatgttgcaagcactcatgtgaattttttttttttaaaaaaaaacccttgaaactgccaacctgcatacaaggaaataatttttcttaatattgtaataagttaggtgtaatgttggtatattttctctgttgtagGAGTGTGGTTCATGCACTGCCATGTAGAACGCCATCAGACTTGGGGCATGGACACTGCGTTCATAGTGAAAAATGGTAAACACCCAGAAGCTCAAGTGCT

upper sequence: GRMZM2G320786_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0122g00690.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------------------tttagatcacgatccattaccacccctaact---acagtatataaatgttgttttattgtatatgtttttttttctcatcacgttg-tgctgcttgtttatt--agGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT
                                           | |  || ||   ||   ||  | |||    | |  |   |||| || |||  |  |||     |   ||     | | |||| |     || | | ||  ||| |||||||| ||||| || || || || || ||   |   ||||||||||||||||||||||| ||||||||||| ||   |||| | ||||||||| |
gtatgttgcaagcactcatgtcctctatttaaaaaaagaaaagaaaaaacaattgcttgaaactgccaacctacataccaaggaaatattttttcttaatattacaataagttaggtgtaatgttggtatattttctctgttgcagGAGTGTGGTTCATGCACTGTCATTTAGAGCGCCATCTGACTTGGGGCATGGACACTGTGTTCATAGTGAAAAATGGTAAACACCCAGAAGCTCAAATGCT

upper sequence: GRMZM2G320786_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0001g00680.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------tttagatcacgatcc-----attaccacccctaactacagtatataaatgttgttttattgtatatgtttttttttctcatcacgttgtgctgcttgtttattagGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT
                                       | | ||  | ||     | | |||||    |   ||    |  ||| ||  || ||  || |   | ||   | | ||   | | |  |   | | |  |||| |||||||| ||||| ||||| || || || ||   |   |||||||||||||||| |||||| ||||||||||| ||   |||| | ||||||||| |
gtatgttgcaagcactcatgttgtctattacacacacaaaaaacaaaaccctccaaactgccaccttgcatatcaaggaaataatttttcttaatattacaatatgttagatttaatattggtatattttctctattgtagGAGTGTGGTTCATGCACTGCCATTTAGAGCGCCATCTGAGTTGGGGCATGGACACTGCGTTCATAGTGAAAAATGGTAAACACCCAGAAGCTCAAATGCT

upper sequence: GRMZM2G320786_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv00s0413g00010.t01 (Vitis vinifera), 3'ss of exon 5
tttagatcacgatccattaccacccctaac-tacagtatataaatgttgttttattgtatatgtttttttttctcatcacgttgtgctgcttgtttatt--agGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT
            |   || | | | || |  | |  |||  |||          ||| |  ||      |   |  | | ||||||    || | ||||  ||| |||||||| ||||| |||||  | || || ||   |   ||||||||||| ||||||||||| ||||||||||| ||   |||| | ||||||||| |
-----------gtatgttgcaagcactcatgtcctctatgaaaaaaaaaaacccttgaaactgccaacataggt-gtaatgttgtgtattttctgtattgcagGAGTGTGGTTCATGCACTGCCATGTAGAACGCCATCTGACTTGGGGCATGGAAACTGTGTTCATAGTGAAAAATGGTAAACACCCAGAAGCTCAAATGTT

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 342

GACCCGGCCACGTACAACCTGGTCGACCCGCCGTACCAGAACACCGTCTCTGTGCCCACGGGCGGCTGGGCTGCGATGCGTTTCCGCGCGGCAAATCCTGgtgagtaccc ... tgtttattagGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

GACCCGGCCACGTACAACCTGGTCGACCCGCCGTACCAGAACACCGTCTCTGTGCCCACGGGCGGCTGGGCTGCGATGCGTTTCCGCGCGGCAAATCCTGgtgagtaccc ... tgtttattagGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT


Block sizes: 20 (upstream exon), 39 (downstream exon)
Score: 3

GACCCGGCCACGTACAACCTGGTCGACCCGCCGTACCAGAACACCGTCTCTGTGCCCACGGGCGGCTGGGCTGCGATGCGTTTCCGCGCGGCAAATCCTGgtgagtaccc ... tgtttattagGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttattgtatatgtttttttttctcatcacgttgtgctgcttgtttattagGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT
                                           cttgttt  CT-rich tract
     ttattgtatatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagatcacgatccattaccacccctaactacagtatataaatgttgttttattgtatatgtttttttttctcatcacgttgtgctgcttgtttattagGTGTGTGGTTTATGCATTGCCACTTCGATCGTCACACGGTGTGGGGCATGGACACTGTGTTCATCGTGAAAAATGGCAAGACCCCAAACGCTCAAATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - -taccacc
- - - - - - - - - - - - - -aactaca
- - - - - - - - - - - - - - - - - - - - - -tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgctgc