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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttggttatgattgccttgaaaatttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA

Basic information

species Zea mays
transcript GRMZM2G037683_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 12
tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttct-agtgct----tggttatgattgccttgaaaatttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA
  ||| |  |||| | ||  ||   | | | |      | |   |  ||| |  ||||||| | | | ||    |||||||  ||| || | ||| ||||| |||||||| || ||||| ||||| ||||| || ||||||||||||||  |||||||||| |||||||||||||||||||||||||||||||||||||||||||
cataa-agtggctattgagcat---cgaagtgcattgcttttttcattttgatggttatttatgaattctattatggttattcttgact-ggaaacttgttacagGTTGTAAAAAGTTTTTCATCTGGTAAACGGGAAGGGGGAGATTTCCTTGCAGCTTCCGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 13
--tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttgg--ttatgattgccttgaaaatttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA
   ||  |    | | |   |   ||     |  |    || | ||  || | | ||  |  | |    ||||   | || |||    ||  ||||  |   ||||||||||||| |||||||| |||||  ||||||| ||||| ||||||||||| |  |||||||| |||||||||||||| || |||||||||||||| |
ttcttttcttttgttcttacaatgaaatgttgtaacagcatgttagg-atctgattgcaaggtatgagacttgagttcattatttgtctgtcaattgat---agGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGATA

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA02G18000.1 (Glycine max), 3'ss of exon 9
---------------------------------------------------------------------------------tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttggttatgattgccttgaaaatttgttt-cagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA
                                                                                  ||  |      | |   |   ||     |  |  | || | ||  || ||| ||  |  | |    ||||  | | |||   |||   ||  |||   ||||||||||||| |||||||| |||||  ||||  | | ||| ||||||||  | |  |||||||| |||||||||||||| |||| ||||||||||||||
gtaactcatattcatgctagccaaaggtggaaatttacttacatgtggattggagaccttgggttatactttttctcatttcttttcttttattcttacaatgaaatgttgtaacaacatgttagg-atctaattgcaaggtatgagacttgagt-tcattat-ttgtctatcagttgatagGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAGAGTGAAGACTTTGTTGCCACCTGCGTTTCACCCAAAGGAGAATGGATTTATTTTGTTGGTGAAGACA

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 13
tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttgg-----ttatgattgccttgaaaatttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA
 ||  ||     | |   |   |||    |       || | ||  || ||| ||  |  | |     |||      | || ||| |  ||| ||||  |   ||||||||||||| |||||||| |||||  ||||||| ||||| ||||||||||| |  |||||||| |||||||||||||| || ||||||||||||||||
-ttttcatctttttttacaatgaagtgttgtagcagcatgttagg-atctaattgcaaggtatgagaattgagttcatcatcatttctctgacaattgat---agGTTGTGAAGAGCTTCTCATCTGGTAAAAGAGAAGGCGGAGACTTTGTTGCAGCCTGTGTTTCACCTAAAGGAGAATGGATTTACTGTGTTGGTGAAGACA

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 12
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 13
tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttggttatgattgccttgaaaatttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA
       ||   |  || |          || |     | |||    |    |    | |   | || |    |     |   ||| ||   | || ||||||||||||||||||||||| |||||  | ||||| ||||||||||| ||||| |  || ||  |||||||||| |||||||| ||  | || |||||||
-----gtaaatttccagcaacggtctcctgcaaatcagtgtca-ttgtcatgccaaaactaagattgttcacatgcttctatattggaatccttttgcagGTTGTGAAGAGTTTCTCATCCGGTAATAGGGAAGGAGGAGATTTTGTAGCAGCATGTGTATCTACAAAAGGAGATTGGATATACTGCATCGGCGAAGACA

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 12
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 13
tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttggttatgattgccttgaaaa---tttgt--ttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA
          |      | |  ||  | |   || ||   |  |   | ||| ||||  |  |   | ||  |||| |        ||||   |||||  | |||||||||||||| ||||| || |||||  ||||||| ||||||||||||||||| |  || ||||| |||||||||||||| |||||||||||||||||||
-----ggtgcgtaaccaaggggaactacgatcagaatggttgtgatttctaaatgtttgtgatgcaggttacttatcaaaaaaaaaaaaaatgtttgtgatgcagGTTGTGAAGAGCTTCTCTTCTGGTAAAAGAGAAGGTGGAGATTTTGTTGCAGCCTGTGTCTCACCCAAAGGAGAATGGATTTATTGTGTTGGTGAAGACA

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S136_176V6.1 (Physcomitrella patens), 3'ss of exon 13
tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttggttatg-attgccttgaaaatttgttt-----cagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA
  | ||| |   | |   ||||  |     | || || |   |    |||  |||  ||   | ||        ||| ||  |||  | |||| || |     ||||||||||||||||| || || || || |||||||| || || ||||| |  ||| | ||||| || ||||| || |||||||||||||||||||||||| 
--tcacagata-tatcctagattcgtcgctc-agcatgtagtatgt-tttcgctgc-atacatggttaccatcaatgtatcccctcaacaattagtatgcatgcagGTTGTGAAGAGTTTGTCTTCGGGAAAACGAGAAGGAGGTGACTTTGTAGGTGCTACTGTTTCCCCGAAAGGGGATTGGATATATTGTGTTGGTGAAGACC

upper sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 13
-------tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttggttatgattgccttgaaaatttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA
       |||   |||  |  |   |  |    ||    |      | ||  |   |    || | |  || ||  |  |||       |    |   |  |  ||||||||||| ||||| || ||||| || |||||||| || || ||||| |  ||| | |||||||| || || || |||||||| ||||||||||||||| 
gtatttctttgggaaattcactgacatgttctgaacttcattggtccccacacgcatg---gtaactattaatgaatacttacagcaatc----agtctgctcccagGTTGTGAAAAGTTTGTCTTCAGGAAAACGAGAAGGAGGTGACTTTGTAGGTGCTACTGTTTCACCCAAGGGGGATTGGATATACTGTGTTGGTGAAGACC

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|211442071|gb|FL307771.1|FL307771
EST:     TTGTCTGCAATAAGACTTCATCAATATTCATCATGACTTTACAAGGACAG                         GTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCA
genomic: TTGTCTGCAATAAGACTTCATCAATATTCATCATGACTTTACAAGGACAGgttatttgaa ... tttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCA




















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: 46 (upstream exon), 49 (downstream exon)
Score: 101

TGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGATCACATTGTTGTCTGCAATAAGACTTCATCAATATTCATCATGACTTTACAAGGACAGgttatttgaa ... tttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 54

TGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGATCACATTGTTGTCTGCAATAAGACTTCATCAATATTCATCATGACTTTACAAGGACAGgttatttgaa ... tttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 41

TGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGATCACATTGTTGTCTGCAATAAGACTTCATCAATATTCATCATGACTTTACAAGGACAGgttatttgaa ... tttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA


Block sizes: 45 (upstream exon), 45 (downstream exon)
Score: 19

TGCATCTGTTAATTCTGTCCATTTATTTCCAAAAAATACTGATCACATTGTTGTCTGCAATAAGACTTCATCAATATTCATCATGACTTTACAAGGACAGgttatttgaa ... tttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttaactgttatttctagtgcttggttatgattgccttgaaaatttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA
 atttaac  putative branch site (score: 19)
                                             tttgtttc  putative PPT
                                      ttgaaaatttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttaacaaaggctgtagaagataagcaaggcgaggatatctcagccatttaactgttatttctagtgcttggttatgattgccttgaaaatttgtttcagGTTGTGAAGAGTTTCTCATCAGGTAAGCGAGAAGGGGGAGATTTTGTTGCAGCTTCAGTTTCACCAAAAGGAGAATGGATATATTGTGTTGGTGAAGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- taacaaa
- - - - - gctgtag
- - - - - - - - -aagataag
- - - - - - - - - - - - - - - - - - - - tcagcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgc