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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatatcagtgatgcaaacatgtgtttccagaatatggtgttgacaactgttgacattccatgtaagctgatcatctcttctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA

Basic information

species Zea mays
transcript GRMZM2G164352_T05
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 7
----gtgatatcagtgatgca-----aacatgtgtttccagaatatggtgttgacaactgttgacattccatgtaagctgatcatctcttctttg--gcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA
     || ||  | | ||||      | ||| |||||      | |    || | || |    | |  | |||   | | ||    | ||||||   ||||||||| || ||||| |||||| |||| ||||| |||||  | ||||| || |||||||||||||| || || || || || ||||| ||||||||||| |
tttaatgctacaactaatgctgtggcagcat-tgtttaacctttttttctttcaaaatttccaagaaactatgcctgtttatgtgtttttctttattgcagGATGCAACAATTGAGCAGCTTCTTCCTATTTTTCTCTCCCTTTTGAAGGATGAATTTCCTGATGTACGCCTAAATATCATAAGCAAGCTTGATCAAGTGA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 7
-------------gtgatatcagtgatgcaaacatgtgtttccagaatatggtgttgacaactgttgacattccatgtaagctgatcatctcttctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA
                | |||  |  |  |  |   ||||     | ||  || ||      |||  |  | |     |     | | | ||||| ||| ||||| || || ||||| |||||| |||| |||||||| ||  | ||||| || ||||||||||| || || || ||||| |||||||| ||||||||||| |
taaaagataatcaacaaaatctattttctaggctattgttatagtagta--gttttatttggtgtaaatgtgcatctcagttctaccttatcttcattg-cagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCTGACGTACGCCTAAACATTATCAGCAAGCTTGATCAAGTGA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA09G31760.1 (Glycine max), 3'ss of exon 7
---------gtgatatcagtgatgcaaacatgtgtttccagaat-atggtgttgacaactgt-tgacattccatgtaagctgatcatctcttctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA
          ||| |    |       | | ||  ||| |   | |  | |  ||    ||       || | | |||  || |  | |  |  ||| |||||||| || || || || ||| | || |||||||| ||| | ||||||||||| |||||||||||  | || || || |||||||| ||||||||||| |
cctaaactcttgaaactgtttccatgtaaaagtaattcaactcttaaagagaggatggatgcaccttcttgcttttaaaatgtttttgtggtggttg-cagGATGCCACAATCGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 7
gtgatatcag-tgatgca-aacatgtgtttccagaatatggtgttgacaactgttgacattccatgtaagc-tga---tcatctcttctttg--------gcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA
   |||  || |  | || || || | ||| |      |  |  ||| | | || |   ||   |||||   |||   |||  ||| | ||         |||||| || || ||||| |||||| |||| |||||||| ||  | ||||| || |||||||| || || || || ||||| |||||||| ||||||||||| |
---ataaaagatagtacacaaaatctattttctaggc-taattgtgatagcagtagttttttggtgtaaatgtgaatctcagttctaccttatcttcattgcagGAAGCAACAATTGAGCAGCTTCTTCCTATTTTCCTTTCCCTTTTGAAGGATGAATTTCCCGACGTGCGCCTAAACATTATCAGCAAGCTTGATCAAGTGA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA07G10000.1 (Glycine max), 3'ss of exon 6
--------gtgatatcagtg--atgcaaacatgtgtt---tccagaatatggtgttgacaactgttgacattccatgtaagctgatcatctcttctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA
         ||| |    |   ||| |||  |   |    ||   || |  |  ||||      ||  |  |   | |||    ||  |        | |||||||||||| ||||| || ||| | || |||||||| ||| | ||||||||||| |||||||||||  | || || || |||||||| ||||||||||| |
ctaaactcttgaaactgttcccatgtaaaagtaactcaactcttaaagagaggattgatgcaccttttcgct---tttaaaaacatttttgtggtggttgcagGATGCTACAATTGAGCAACTTCTGCCTATTTTCCTTTCTCTTTTGAAAGACGAGTTTCCTGATGTCAGGCTAAATATTATCAGCAAGCTTGATCAAGTGA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 7
lower sequence: AT1G13320.2 (Arabidopsis thaliana), 3'ss of exon 7
-----------gtgatatcagtgatgcaaac-atgtgtttccagaatatggtgttgacaactgttgacattccatgtaagctgatcatctcttctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA
              |||| ||  |  |  || |||| |||| | |  | | | || |     | |       | | |||  ||    |    |   |  |||||||| || ||||| || ||| ||||||| || || ||| | ||||||||||||||||||||||| ||  | ||||| |||||||||||||| ||||| |
cgcaacaataatctatataagaaaacctcactatgtttttctaca-caagatattta-gttggattttgcagcttttaacttggcattgatattcatttcagGATGCAACAATTGAGCATCTTCTTCCAATCTTTCTTTCTCTATTGAAAGACGAATTTCCTGATGTACGCTTAAACATTATCAGCAAACTTGACCAAGTGA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 7
lower sequence: Vv17s0000g03870.t01 (Vitis vinifera), 3'ss of exon 8
-----------------gtgatatcagtgatgcaaacatgtgtttccagaatatggtgttgacaactgttgacattccatgtaagctgatcatctcttctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA
                  ||| ||     ||| |   || | | ||||     |||| |||    |||||     |  |  |||  |    |||| |  |     |||| || || || || || ||| | || |||||||| ||| || | ||||| || ||||||||||| ||||| || || |||||||| ||||||||||| |
tttggtagattttttccctgagatgttctatggagtgatctatatcca----ctggt-ttggtctctgtttgtcatttaattaatata--tatctttattcctatagGACGCAACAATAGATCAACTTCTGCCCATTTTCCTTTCTCTGCTTAAAGATGAGTTTCCTGATGTCCGACTGAATATTATCAGCAAGCTTGATCAAGTAA

upper sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 7
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 6
---gtgatatcagtgatgcaaacatgt-gtttccagaatatggtgttgacaac----tgttgacattccatgt---aagctgatcatctcttctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA
    |||| |||   || ||||  | | |       | | |  |||| | | |    |  |   |||  || |   ||  |  || |   | ||   ||||||||| || ||||| || ||| |||||||||| || ||| | ||||| || || ||||||||||| ||||| || || || ||||| ||||||||| | |
caattgatctca-caattcaaatttattgggagtgcatttttctgttaagatcatgtttcttgaattggatttctgaactttgtcttggttgctgatgcagGATGCAACAATTGATCAACTTCTTCCAATTTTTCTTTCTCTTTTGAAGGATGACTTTCCTGATGTACGACTAAATATCATTAGCAAGCTTGATCAAATAA

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|87156353|gb|DY401142.1|DY401142
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|67016540|gb|CO445289.1|CO445289
EST:     GTTCAGCTTTACCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|87157118|gb|DY401907.1|DY401907
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|26558526|gb|CA830761.1|CA830761
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|67017790|gb|CO446539.1|CO446539
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|32933390|gb|CF038202.1|CF038202
EST:     GGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|211403483|gb|FL417168.1|FL417168
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|22546073|gb|BU098394.1|BU098394
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|31349427|gb|CD433784.1|CD433784
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAA                         GATGCTACCAT
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCAT
EST: gi|42491785|gb|CK700831.1|CK700831
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|23357737|gb|BU645386.1|BU645386
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|67022121|gb|CO450870.1|CO450870
EST:     TATGGGCATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: TATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|31356642|gb|CD440999.1|CD440999
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGT-CCAATTTTTCCTCTC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTT-CCTCTC
EST: gi|211315613|gb|FL415838.1|FL415838
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|26560084|gb|CA832319.1|CA832319
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|67039515|gb|CO465770.1|CO465770
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|31355734|gb|CD440091.1|CD440091
EST:     GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
EST: gi|13315895|gb|BG410243.1|BG410243
EST:     G-TCAGCTTTAGCCTCAG-GATTATGGGAATGGCTCCTGTACTGGGAAAG                         GATGCTACCATTGAACAGC-TGTTCCAATTTTCCTCTCTTTGTTGAAAGAC
genomic: GTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGAC

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: 313

GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 326

GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 263

GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 246

GAATTGTCATCAGATTCATCCCAGCATGTTCGTTCAGCTTTAGCCTCAGTGATTATGGGAATGGCTCCTGTACTGGGAAAGgtgatatcag ... tctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggtgttgacaactgttgacattccatgtaagctgatcatctcttctttggcagGATGCTACCATTGAACAGCTTGTTCCAATTTTCCTCTCTTTGTTGAAAGACGAATTTCCTGATGTTCGACTTAACATAATCAGCAAACTTGATCAAGTTA
                                     tcatctcttcttt  CT-rich tract