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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcttaatgtttacacgatagtagtagaatgatgaatatgttcatagggttgtcagtttccttttaactaacaataccatgcattcttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG

Basic information

species Zea mays
transcript GRMZM2G171435_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g55600.1 (Oryza sativa), 3'ss of exon 5
--ggcttaatgtttacacgatagtagtagaatgatgaatatgttcatagggttgtcagtttccttttaactaacaa-taccatgcattcttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
     || || |    || |||  | || | ||    ||   || |     || || | ||   | |||  | ||| |   |        || || ||||||||| || ||||| ||||| ||||| || || ||||| ||||| |||||||||||||||||||||||||||||||| |||||||| |||||||||
taaatttcatttgcttacaata-cactatactggc--attactttaggacattatctggtttactctaataagcaaatgataaaagacaatctttttctgcagTCTTCAGTTCTCCATTCACAACCAAAATCCACTGTAGGAACCCCTGCTTATATTGCACCTGAAGTTCTGTTGAAGAAAGAATACGATGGCAAG

upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G20610.4 (Glycine max), 3'ss of exon 5
-ggcttaatgtttacacgatagtagtagaatgatgaata-tgttcatagggttgtcagtttccttttaactaacaataccatgcattcttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
     || ||  |  || |   |||  ||    ||  |  ||||  |   ||| | |||||  ||||  | |  |||   ||  ||  |    | |   ||||| || || |||||||| ||||| ||||||||||| ||||| ||||| |||||||| || |||||  || ||||| |||| ||||||||||||
tacaatagtggatttacaactatagatgatcattgtttcctgttgtttttgttttgagtttttttttcccca--aatctgattgatggtgtgatttgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGCTGAAACAAGAGTATGATGGCAAG

upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA11G06250.1 (Glycine max), 3'ss of exon 5
ggcttaatgtttacacgatagtagtagaatgatgaatatgttcat--agggttgtcagtttccttttaactaacaataccatgcattcttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
   |  | ||   |    ||  ||||     |     | || |||  |  ||||     || || |   |||  |||   ||  ||| |   || |  |||||| || || |||||||| ||||| ||||||||||| ||||| || || |||||||| || |||||  || ||||  |||| ||||||||||||
aaatagaggtcatccatgtacaagtaatgacacatcaaggtccattaatagttgatcaattactatatcctacaaatctaatagatttt--gttattggcagTCTTCGGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG

upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA01G39020.2 (Glycine max), 3'ss of exon 5
--ggcttaatgtttacacgatagtagtagaatgatgaatatgttcatagggttgtcagtttccttttaactaacaataccatgcattcttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
      |   ||       ||  || |  | |    |  || |  || |  |||     || || |   ||   |||   ||  ||| |   || |  |||||| || || |||||||| ||||| ||||||||||| ||||| || || |||||||| || |||||  || ||||  |||| ||||||||||||
tttttctttcgtcctttgtattctattttattttaaagaatttgaattgttttgatcaatttctgtatcctgcaaatgtaatagatttt--gttattggcagTCTTCCGTGCTTCATTCACAACCTAAGTCAACTGTGGGAACTCCAGCATATATTGCTCCAGAAGTATTGCTGAAGCAAGAGTATGATGGCAAG

upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA05G09460.1 (Glycine max), 3'ss of exon 5
ggcttaatgt-ttacacgatagtagtagaatgatgaatatgttcatagggttgtc--agtttccttttaactaacaataccatgcattcttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
    || ||  ||  || | | |||    ||||    | |||   |    ||||   |||||  ||||    |  |||    |  ||  |    |     ||||| || || |||||||| ||||| ||||||||||| ||||| ||||| |||||||| || |||||  |||||||| |||| ||||||||||||
---atagtggattttacaacaatagatagatgaattgtttgtagttgtatttgtttgagttttttttttctcacaaatctgtttgatggtgtgattcgcccagTCTTCAGTGCTTCATTCACAACCAAAGTCAACTGTGGGAACTCCTGCATATATTGCTCCAGAAGTATTGTTGAAACAAGAGTATGATGGCAAG

upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT5G66880.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------ggcttaatgtttacacgatagtagtagaatgatgaatatgttcatagggttgtcagtttccttttaactaacaataccatgcattcttcattctct----gcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
           |  ||  ||||     | ||  || |     |    | || |       ||||||  |||   |    |   ||     |   || | ||||   |     ||||| |||||||||||||| ||||| |||||||||||||| || ||||| || || || || || || ||| |     | |||||||||||||||
gtatcacaaatgattt--tgttcttttggtatcagaaactatacacttgtggttcctccattgtcatgttcaaatgtgtttttaaagtgtttgcttatgcatttctttttgacagTCTTCTGTTCTTCATTCACAACCAAAGTCAACTGTTGGTACTCCTGCATACATCGCTCCAGAGGTACTGCTTCGTCAGGAATATGATGGCAAG

upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT3G50500.1 (Arabidopsis thaliana), 3'ss of exon 5
ggcttaatgtttacacgatagtagtagaatgatgaatatgttcatagg--gttgtcagtttccttttaactaacaataccatgcattc-ttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
  ||||  ||| |  |  |  ||     |||       |  | |  |   ||| ||  |||  |||   || | | ||  |   || | ||  || ||| ||||| |||||||||||||||||||| |||||||||||||| || ||||| || |||||||| ||  ||||  |   | | |||||||||||||||
-tcttatcgttcatgctctt-tacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctca-agtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG

upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT3G50500.2 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------------------------ggcttaatgtttacacgatagtagtagaatgatgaatatgttcatagg--gttgtcagtttccttttaactaacaataccatgcattc-ttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
                                                                                         ||||  ||| |  |  |  ||     |||       |  | |  |   ||| ||  |||  |||   || | | ||  |   || | ||  || ||| ||||| |||||||||||||||||||| |||||||||||||| || ||||| || |||||||| ||  ||||  |   | | |||||||||||||||
gtttgttttctgaattctaagtttatatatgctactgtatggccaagcgcagaacagcgggggacatcttgtgattcctcgttgtgcttcttatcgttcatgctctt-tacctacatgtgtttcctactaagtgtctgttttcgctttgatttctgctca-agtattaactatgcgtttcttttcttcagTCTTCTGTTCTTCATTCCCAACCAAAGTCAACTGTTGGTACTCCTGCATACATTGCACCAGAGATTCTTCTTCGACAGGAATATGATGGCAAG

upper sequence: GRMZM2G171435_T02 (Zea mays), 3'ss of exon 5
lower sequence: AT4G33950.1 (Arabidopsis thaliana), 3'ss of exon 5
ggcttaatgtttacacgatagtagtagaatgatgaatatgttcatagggttgtcagtttcctt---ttaactaacaataccatgcattcttcattctctg-cagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
                                    ||| ||   |    | ||||   |  |   |||  ||  |   | | || || |   |||| |  |||||||| ||  | ||||| ||||| || |||||||||||||| |||||||| || || ||||| ||| |  | || |||||||||||||| |||
-----------------------------------gtatctttgaaaacatttcagaaactctgagttagttagtatctctaagctttgtgttttctttttcagTCATCAGTGTTACATTCGCAACCAAAATCAACTGTTGGAACTCCTGCTTACATCGCTCCTGAGGTTTTACTAAAGAAAGAATATGATGGAAAG

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|211499753|gb|FL295241.1|FL295241
EST:     ATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAG                         TCATCTGTTCTTCATTCGCAACCGAAGTCAACTGTTG
genomic: ATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAGgttcttacac ... ttctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTG
EST: gi|32859143|gb|CD998824.1|CD998824
EST:     ATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAG                         TCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTAT
genomic: ATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAGgttcttacac ... ttctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTAT
EST: gi|6022633|gb|AW067445.1|AW067445
EST:     ATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAG                         TCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTAT
genomic: ATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAGgttcttacac ... ttctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTAT
EST: gi|148932906|gb|EE285698.2|EE285698
EST:     ATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAG                         TCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTAT
genomic: ATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAGgttcttacac ... ttctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTAT
EST: gi|78107855|gb|DV526273.1|DV526273
EST:     ATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAG                         TCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTAT
genomic: ATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAGgttcttacac ... ttctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTAT

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: 48 (upstream exon), 47 (downstream exon)
Score: 115

CAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAGgttcttacac ... ttctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 47

CAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAGgttcttacac ... ttctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 114

CAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAGgttcttacac ... ttctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 71

CAAGTATGCCACCGTGATTTGAAGCTGGAGAACACACTTCTAGATGGGAGTGATGCTCCTCGCTTGAAGATATGTGACTTCGGTTATTCCAAGgttcttacac ... ttctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agggttgtcagtttccttttaactaacaataccatgcattcttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG
                    aactaac  putative branch site (score: 71)
                                    cattcttcattctct  putative PPT
                ttttaactaacaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcttaatgtttacacgatagtagtagaatgatgaatatgttcatagggttgtcagtttccttttaactaacaataccatgcattcttcattctctgcagTCATCTGTTCTTCATTCCCAACCGAAGTCAACTGTTGGAACACCTGCTTATATTGCACCTGAAGTTCTGTTGAAAAAAGAATATGATGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA