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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcaaaatgttccaaatagaaattctattcctctgccgcgacgttacttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG

Basic information

species Zea mays
transcript GRMZM2G045330_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 8
gtattgcaaaatgttccaaatagaaattctattcctctgccgcga-cgttacttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
||||||||  |||||    |    |  | | ||  | |||| ||    || ||| |    |  ||||||    | |||||||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||||  ||||||||||| ||||||||||| |||||||||
gtattgcatgatgttgtgcaagctacatttttttttttgccacgggtatttcttgtgttaacttgatattatggcagGTTCTTGGTACTCCAACCCGTGAGGAAATACGATGCATGAACCCCAACTATACTGAGTTCAAATTTCCTCAGATTAAGGCTCATCCTTGGCACAAG

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA04G06760.1 (Glycine max), 3'ss of exon 8
---------gtattgcaaaatgttccaaat-----agaaattctattcctctgccgcgacgttacttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
         || |||  |  | ||  |  |     ||  || | || | | |      |  | || | |||  |  |  | |   || |||| ||||| || || || || |||||  |||| || ||||||||||| || | ||| || ||||||||||||||||| || || ||||||||||||
gtacaattggtgttgatatgtattgtatgttccttagtcatgccatccttgtcattataaatcacct-ttgtaaaattttgtat-tgcagGTGCTTGGCACGCCCACTCGAGAGGAAGTACGCTGTATGAATCCCAATTACAATGACTTTAGGTTTCCTCAGATAAAAGCACACCCATGGCACAAG

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G06850.1 (Glycine max), 3'ss of exon 8
---------gtattgcaaaatgttccaaat-----agaaattctattcctct-gccgcgacgttacttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
         || ||   |  | || ||  |     ||  || | || | | |   |   ||    |||  |   || |  |||   || |||| ||||| || || ||||| |||||  |||| || ||||||||||| || | ||| || |||||||| |||||||| || || ||||||||||||
gtacaattggtgttaacacgtattgcatgttccttagtcatgccatccttgtcatcataactcacctttgtaaaattttgtat---tgcagGTGCTTGGCACACCCACCCGAGAGGAAGTACGCTGTATGAATCCCAATTACAATGACTTTAGGTTTCCACAGATAAAAGCACACCCATGGCACAAG

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
---------gtattgcaaaatgttccaaatagaaattctattcctctgccgcgacgttacttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
          |  |  |  |   ||   || ||  ||  |        | ||   | || |||||   ||||  |   | |||||||||||||||||||||| || ||||| || || || ||||| || || ||||| ||||| || || |||||||| || |||||||| |||||||||
gtgatgtcccttctatatgagtgtctccatgga--ttgcagaatatatctgcagagataattatttagatgtctt---cttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 8
gtattgcaaaatgttccaaatagaaattctattcctctgccgcgacgttactt-----attggtatgtga---tatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
     |  |  | |     |||  | |  |       |  |   |  |  |||     ||   ||| |     | | | ||||||||||||||||||| || || ||||| || || |||||||| || || ||||| || || || || |||||||| || |||||||| |||||||||
-----gtgatgtctctttgatattagtgttgccatgattgcagaatatatcttcagagatcattatttaggtgtcttcttgtagGTTCTTGGTACTCCGACTCGAGAGGAAATCCGTTGCATGAACCCAAATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 8
gtattgcaaaatgttccaaatagaaattctattcctctgccgcgacgttact-tattggt-atgtgatatgcctgt--agGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
     |  || | |||       | ||| | ||     | |    | |  || |  |  | ||||| | ||   ||  ||||||||||||||||||| || || || || ||||||||||| || ||||| || || ||||| || || || || || || || || ||||| |||
-----gtgaactcttcttttattatattttgttttggcgtcatttcctgtctgtgctcatgatgtgctgtgttggtttagGTTCTTGGTACTCCAACTCGCGAAGAAATCCGGTGCATGAACCCAAACTACACAGACTTCAGATTCCCACAAATCAAAGCCCACCCTTGGCATAAG

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: AT4G18710.1 (Arabidopsis thaliana), 3'ss of exon 7
----gtattgcaaaatgtt--ccaaatagaaattctattcctctgccgcgacgttacttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
    | ||    ||| | |       |  |||||  |||| |  ||  | |  |  || | || |||      ||     ||||||||||||| ||||| || || || || || || ||||||||  | || || || ||||||||||| ||||||||||| ||||| |||||||||
gtaagaatctttaaacgatgattccttgcaaattacattctttggctacaaaatc-ctcactg-tatagttgttgtacacagGTTCTTGGTACACCAACTCGAGAAGAAATCCGTTGTATGAATCCACATTACACAGATTTCAGGTTTCCACAGATAAAGGCACATCCCTGGCACAAG

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
gtattgcaaaatgttcca--aatagaaattctattcctctgccgcgacg-ttacttattggtatgtgatatgcct----gtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
||   |||  || |       |||  |       || |||||   | |  | |  || |  | ||||||     |     ||||||||||||||||||||  | || || || || || ||||| || || |||||||| ||||||||||||||||| || |||||||| |||||||||
gtgcagcatcatttcttgttgatattatcgaggatcatctgctatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 3'ss of exon 8
gtattgcaaaatgttccaaata-gaaattctattcctctgccgcga---cgttacttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
||        || ||     |  |||||  | |   ||||  |       ||||  |  | | || |  | ||   | ||||||||||||| ||||| || || || || || || |||||||| |  |||||||| || |||||||| |||||||| || || || |||||||||
gtgcaatttgatttttagtgtttgaaatcatgtagttctggtgatcatttgttaaattcttgcattttgtctggtggcagGTTCTTGGTACACCAACGCGGGAAGAAATTCGCTGTATGAATCCGAGTTATACTGATTTTAGGTTTCCACAGATAAAAGCACACCCTTGGCACAAG

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------------------------------------------------------------------------gta-ttgcaaaatgt--tccaaatagaaattctattcctctgccgcgacgttacttattggtatgtga-tatgcctgt-agGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
                                                                                                                  ||| ||||    |||  |   | |    | |    |    ||          |||||| ||||  ||  | |   ||| ||||  | || || || || || |||||||||  |||||||||||| ||||| || ||||||| ||||||||| || ||||||||||| |||||||||
gtagcttacatatggtagatgttgaggaagtgcaggggtctacagcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgcgttgaaaggttgtagctggtacttgctcggtgtgatgttagttatgacttcgctagaatggatatgtaggacttatgggtagttgggtgttaatgttagGTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAG

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------gtattgcaaaatgttccaaata--gaaattctattcctctgccgcgacgttacttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
                                                 ||||    |||  |   |   | | |  |||    |||  |    ||   ||||||        | |    | ||||  | || || || || |||||||||||   |||||||||||| ||||| || ||||||| |||||| || || |||||||| ||||||||||| 
gtagggcacaggcgatgcacggtgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgggagtgttatgatgctgt-ggagtgtatgttattgaggaaaagttttgtggcagGTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAA

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------------------------gtattgcaaaatgttccaaatagaaattctattcctctgccgcgacgttac-ttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
                                                     |  |    | |||| |     |   || |  | || ||  | |    ||  ||||||    ||  |      | ||||  | || || || || ||||||||||||  |||||||||||| ||||| || ||||||| |||||| || || |||||||| || |||||||| 
gtagggcacaggcggtgcacggcgttgtgttgaagggtggcgtacttgcttgctggttgtgactgttgcgg--gggtgttatgatgctgtggagtgtgagtatgttattgaggagtacttgtgtggcagGTGTTGGGAACACCGACTCGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCGTGGCACAAA

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------------gtattgcaaaatg--ttccaaata-gaaattctattcctctgccgcgacgttact-tattggtatgtgatatgcctgt---agGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
                                                |  | ||    ||  ||  |  |  |  ||  | ||| | |     |    ||     |||    |   | | | |||   ||||| | || || || || |||||||||||   |||||||||||| ||||| || ||||||| |||||| || || ||||| || || |||||||| 
gtgggacacacgtggtacacgttgtttgtgtggaagggtcgccttctgggttggcggtttggtttgtagctgtggtatcttgttcgtgttggatgtgagtatggcgttgaccagacgtttccgtgtggcagGTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAA

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 8
-------------------------------------------------------------------------------------------------------------------gtattgcaaaatgttccaaatagaaattctattcctctgccgcgacg-ttacttattggtatgtgat-atgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
                                                                                                                   |  | |     |||| |   |   |   | |      | | |    | |||    | ||    || | |||     ||||  | || || || || ||||||||||||  |||||||||||| ||||| || ||||||| ||||||||| || |||||||| || |||||||||
gtatgttatacatggtagagtggaagcatatggagctgaagtcgtttgtactgatgtttgatgtgtatcgattaaaagtattgtattatatttaaagatgttagctgctcttgttgcttcgggtggtgttgcgg-tgatagcgcaagagtgatactgtagagcttatgagtaggcggatggtgatgttgacagGTGTTAGGGACACCTACACGTGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCACCCGTGGCACAAG

upper sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 8
gtattgcaaaatgttccaaatagaaattctattcctctgccgcgacgttacttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
                    | |   || |   | | ||  |    |   || ||     || ||  |||  | |||||||||| || || || || ||||||||   ||| |||||||||||||| || || |||| ||| ||||| || ||||| ||||| |||||||||
--------------gttggctcgttgtttttgccttatggtggctgggcgctcataaagttg-gacttgc--gcagGTTCTTGGAACCCCTACTCGCGAGGAGATCAAGTGTATGAATCCCAACTACACGGAATTCAAGTTCCCTCAAATCAAGGCCCATCCTTGGCACAAG

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|20508268|gb|BQ279947.1|BQ279947
EST:     CACTATTTCCAGGAGAGAGCGCTGTTGATCAGTTGGTAGAGATCATCAAG                         GTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTAT
genomic: CACTATTTCCAGGAGAGAGCGCTGTTGATCAGTTGGTAGAGATCATCAAGgtattgcaaa ... atgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTAT
EST: gi|67028577|gb|CO457326.1|CO457326
EST:     CACTATTTCCAGGAGAGAGCGCTGTTGATCAGTTGGTAGAGATCATCAAG                         GTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTAT
genomic: CACTATTTCCAGGAGAGAGCGCTGTTGATCAGTTGGTAGAGATCATCAAGgtattgcaaa ... atgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTAT

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: 42 (upstream exon), 48 (downstream exon)
Score: 212

CCACTATTTCCAGGAGAGAGCGCTGTTGATCAGTTGGTAGAGATCATCAAGgtattgcaaa ... atgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 89

CCACTATTTCCAGGAGAGAGCGCTGTTGATCAGTTGGTAGAGATCATCAAGgtattgcaaa ... atgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 102

CCACTATTTCCAGGAGAGAGCGCTGTTGATCAGTTGGTAGAGATCATCAAGgtattgcaaa ... atgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 71

CCACTATTTCCAGGAGAGAGCGCTGTTGATCAGTTGGTAGAGATCATCAAGgtattgcaaa ... atgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaaattctattcctctgccgcgacgttacttattggtatgtgatatgcctgtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG
                          ttacttatt  TA-rich tract