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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctatgagataatatgaaatacttcaaacttctgttttgttgatcatttttcacattttatctgtcttcacaactaatggtgcattttccttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG

Basic information

species Zea mays
transcript GRMZM2G128877_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g07870.1 (Oryza sativa), 3'ss of exon 12
agctatgagataatat-gaaatacttcaaac-ttctgttttgttgatcatttttcacattttatctgtcttcacaactaatggtgcattttccttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG
|  ||  || ||| || |  |||  |||  | |  || ||| ||||  || | |   || |||  | |  | |     ||||   ||||||  ||  ||||||||||||||||||| |||||||||||||| ||||| ||||||||  |  ||||||| || ||||||||||||||||| || |  || || ||||||||| 
acttaaaagttaagattgttataactcattcgtgttgattttttgaatatctattttatgttaa-tattctaatgggcaatgccacatttttgtta-tccagGCTGAAATGCCTGCAGATAGTGGTTACCCTGCTTATTTGGCTGCAAGACTGGCATCTTTCTATGAACGTGCTGGTAAAGTAAGGTGTCTTGGAAGTCCAA

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 13
----------------------------------------------------------------agctatgagataatatgaaat--acttca-aacttctgttttgttgatcatttttcacattttatctgtcttca--caac------taatggtgcattttccttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG
                                                                | || |        |  |  |  |||  | || || | |    ||   |||    |||||   |   | | |    |||       | ||| |    ||  |||    ||||| ||||||||||| |||||||| || || || ||| | ||||| ||||| || || || |||||||||||||| ||||| ||||| || ||| | || |
gtgagaaagatttattttttgtgcttaaaatacatatattttgtagccttactttatgatattgaactttctttcttgactagtttaactagacaatttatataccattaggcatgagacacatgggaatggacattgatcaatgtattttgatgatattgttgtcttc-cacagGCAGAAATGCCTGCAGATAGTGGATATCCTGCATACCTTGCTGCACGTTTAGCCTCTTTCTATGAACGTGCTGGGAAGGTAAAATGTCTAGGAGGCCCTG

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 13
agctatgagataatatgaaatacttcaaacttctgttttgttgatcatttttcacattttatctgtcttca--caac------taatggtgcattttccttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG
     |    || | | || ||     || || | |    || | |||    |||||   |   | | |    |||       | ||| |||  ||  |||    ||||| ||||||||||| |||||||| || || || ||| | ||||| ||||| || || || |||||||||||||| ||||| ||||| || ||| | || |
----cttgactagtgt-aactagac--aatttatataccattaaccatgagacacatgggaatggacattgatcaatgtattttgatgatgctgttgtcttc-cacagGCAGAAATGCCTGCAGATAGTGGATATCCTGCATACCTTGCTGCACGTTTAGCCTCGTTCTATGAACGTGCTGGGAAGGTAAAATGTCTTGGAGGCCCTG

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 9
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 13
agctatgagataatatgaaatacttcaaactt-ctgttttgttgatcatttt--tcacattttatctgtctt---cacaactaatgg---tgcattttccttggtcc---agGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG
          |||| | |     ||||   || || | | | || || | ||   | ||| | |  | ||||   | ||  | || |      ||||| ||| ||     ||||||||||||||||||| ||||| || ||||| ||  | || || ||||| ||||| || ||||||||||||||||| || ||||| || ||  | ||||
---------gtaatcttatgcgtttcacttttgctatatggatgttcgtgttgtcctcatctcacttttctttttctcagtttattgacacctattttgctttgttttatagGCTGAAATGCCTGCTGACAGTGGATATCCAGCCTATCTAGCAGCACGTTTAGCATCTTTCTATGAACGTGCTGGTAAAGTAAAATGTCTTGGTGGACCAG

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 9
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 3'ss of exon 13
---agctatgagataatatgaaatacttcaaacttctgttttgttgatcatttttcacattttatctgtcttcacaactaatggtgcattttccttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG
      | |   ||  |       |  |   |        |     |    | |||| || | || | | |||  |  |     || || |    || | |||||||| |||||||| || |||||||||||||||||| | |||||  | || || || || |||||| | || || || || || || ||||| || ||  
ttacattgtattatccttcagttaaggtaggaacggaagatgaggaaatgctcttcagatatcatgt-ttttcttatttccaactgtatgtgg--tgctgcagGCTGAGATGCCTGCGGACAGTGGTTACCCAGCTTACCTAGCTGCAAGATTAGCTTCTTTCTATGAAAGAGCAGGGAAAGTTAAGTGTCTGGGGAGCCCGA

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 9
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 13
--------------------------------------------agctatgagataatatgaaatacttcaaacttctgttttgttgatcatttttcac---attttatct-gtcttcacaactaatggtgcattttccttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG
                                            | ||      ||  ||| | |  || |     | || | |       || | ||    || | ||   | ||  |  ||     ||   | |    |  | |||||||| ||||||||||| |||||||||||||| ||| | |||||  | ||||| |||||||||||| | || || || |||||||| |||||||| ||| 
gtatgttctcaggactttcctttggtgttttttttagggtttcaaacttgttagtatcatgtatttatttatgga-cagtataggcaggttttgtccatgcaatgtcattcagactctaagacatgcagttactctgtggttttgcagGCTGAGATGCCTGCTGACAGTGGTTACCCAGCGTACCTTGCTGCAAGGTTGGCCTCCTTTTATGAAAGAGCAGGAAAAGTGAAATGTCTGGGAAGCCCAA

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 9
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 3'ss of exon 13
agctatgagataatatgaaatacttcaaacttctgttttgttgatc---atttttcacattttatctgtcttcacaactaatggtgcattttccttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG
    || | ||   |  | ||      |     |     |   ||    |  |   || ||  |  | | ||   ||    || | || ||     | | |||||||| ||||||||||| |||||||| ||||||||| | |||||  | || || || || |||||| | || || || ||||| || |||||||| ||  
--tcataatatttaaaaatatttgctcagggcatagccagacaattcagaaatgctactttccagatattttgctaatatgtgat-cacttgtggggcttcagGCTGAGATGCCTGCTGACAGTGGTTATCCAGCTTACCTTGCTGCAAGATTAGCTTCTTTCTATGAAAGAGCCGGGAAAGTGAAGTGTCTGGGAAGCCCGA

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 9
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 12
agctatgagataatatgaaatacttcaaacttctgttttgttgatcatttttcacattttatctgtcttcacaactaatggtgcattttccttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG
                                              |  | ||  ||||| | | | |||  || |     | ||    ||  |   ||||| ||||||||||| || |||||||| ||||| || |||| ||| ||||||||  | ||||| || || ||||| ||||| |||||||| || ||||| |
--------------------------------------------gtaagtctctgattttctttctattcctaatt-----tacaaacgccgcg---cagGCCGAAATGCCTGCCGACAGTGGTTATCCAGCGTATTTGGGTGCACGTTTGGCTACGTTTTACGAGCGGGCTGGAAAGGTTAAATGCCTTGGTAGTCCCG

upper sequence: GRMZM2G128877_T03 (Zea mays), 3'ss of exon 9
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 13
agctatgagataatatgaaatacttcaaacttctgttttgttgatcatttttcacattttatctgtcttcacaactaatggtgcattttccttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG
                                              |  | ||  ||||| | | | |||  || |     | ||    ||  |   ||||| ||||||||||| || |||||||| ||||| ||  ||| ||| ||||||||  | ||||| || || ||||| ||||| |||||||| || ||||| |
--------------------------------------------gtaagtctctgattttctttctattcctaatt-----tacaaacgccgcg---cagGCCGAAATGCCTGCCGACAGTGGTTATCCAGCGTATCTGGGTGCACGTTTGGCTACGTTTTACGAGCGGGCTGGAAAGGTTAAATGCCTTGGTAGTCCCG

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|32831320|gb|CD970998.1|CD970998
EST:     ATCTCA-GGCG-TTG                         GCTG-AATGCCTGCTGATAGT-GTTACCCAGCTTACTT-GCTGCGCGTTT-
genomic: ATCTCAGGGCGTTTGgtatgctact ... cttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTG
EST: gi|211154401|gb|FL123520.1|FL123520
EST:     ACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTG
genomic: ACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGGGCGTTTGgtatgctact ... cttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTG
EST: gi|33092495|gb|CF052489.1|CF052489
EST:     ACTCCACCTCACGATGGGCTGAGGCTNTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTG
genomic: ACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGGGCGTTTGgtatgctact ... cttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTG
EST: gi|31360171|gb|CD444528.1|CD444528
EST:     ACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGGGCGTTTG                         GCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTG
genomic: ACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGGGCGTTTGgtatgctact ... cttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTG

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: 405

AATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGGGCGTTTGgtatgctact ... cttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 698

AATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGGGCGTTTGgtatgctact ... cttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 565

AATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGGGCGTTTGgtatgctact ... cttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 579

AATTGCCGAGTATTTTCGTGATATGGGCTACAACGTTAGTATGATGGCTGACTCCACCTCACGATGGGCTGAGGCTTTGCGTGAGATCTCAGGGCGTTTGgtatgctact ... cttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttttcacattttatctgtcttcacaactaatggtgcattttccttggtccagGCTGAAATGCCTGCTGATAGTGGTTACCCAGCTTACTTGGCTGCGCGTTTGGCATCCTTTTATGAACGTGCTGGTAAGGTGAAATGCCTGGGAAGTCCAG
                           aactaat  putative branch site (score: 579)
                                      cattttcctt  putative PPT
        acattttat  TA-rich tract