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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtcatagagctccatcttttttgaaaaaaaaatctttaatccatatttattattaaacactaaattgacgacttggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA

Basic information

species Zea mays
transcript GRMZM2G056975_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os01g01710.2 (Oryza sativa), 3'ss of exon 8
gtgtcatagagctccatcttttttgaaaaaaaaatctttaatccatatttattat-taaacactaaattgacgacttggt-cttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA
        | | |     |    |   | ||   |  | |   ||| ||     | |   ||||||| |||  ||||| | | |  |||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||| |||||||| |||||||||||||||||| ||||||
--------gtgtttgcagtaaactttcagaattttactgaggtcatgttggcagtatttgcactaaaatgatcacttgattcatacagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATACGATGACATTGAAATTGTGATCCACCCACAATCTATCATACACTCTATGATTGAAA

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G09740.1 (Glycine max), 3'ss of exon 8
------------------------gtgtcatagagctccatcttttttgaaaaaa-----aaatctttaatccatatttatta-ttaaacactaaattgacgacttggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA
                         | |   |       | | |||||  |||       || | | |  |    ||||  ||  || |   ||||||    |       |   ||||| ||||||| |||||||||||||| || ||||| ||||| |||||| | ||||||||||| ||||| ||||| || |||||||| || ||| ||||||
gtttgtttctttttttatgtcaacatattggacgcaaatagcctttttataaatctgtttaattatgtggtatgaatttcctagctataaggtaaatttcttatacttcttcacagGGTCTAGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTATGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAA

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA05G02190.1 (Glycine max), 3'ss of exon 8
---------------------gtgtcatagagctccatcttttttgaaaaaa-----aaatctttaatccatatttatta-ttaaacactaaattgacgacttggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA
                      | |   |       | |  ||||  |||       || | | |  |    ||||  ||  || |   ||||||            |   ||||| ||||||| |||||||||||||| || ||||| ||||| || ||| | ||||||||||| ||||| ||||| || |||||||| || ||| ||||||
gtttgcttctttttttatgtcatattgaatgaaaagagccattttataaatctgtttaattatgtggtatgaatttcctagctataaggtaaatttcttctgcttcttcacagGGTCTAGAAGTAATTGAAGCACATTACTTGTTTGGAGCTGACTACGATCATATTGAGATTGTCATTCATCCACAATCAATCATACATTCAATGATTGAAA

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv17s0000g08390.t01 (Vitis vinifera), 3'ss of exon 8
--------gtgtcatagag-ctccatcttttttgaaaaaaa--aatctttaatccatatttattattaaacactaaattg-----acgacttggtctt--------gtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA
         | |  | | | ||| ||  ||  | | |   |  ||| | | |   |   |  | | ||    || | |||     |  || | || ||          ||||||||||||||||||||||||| ||| | ||||| |||||||||||||| ||||||||  | ||||| ||||| ||||||||||| |||||||| ||||
gtttgtcccttttttggtgtctctattcttgattacatgcaccaatatgtgaatgaatctactcactatggtctgagttgcaacaaataccttgttttcctttttgacagGGTTTAGAAGTTATTGAAGCACACTATCTGTTTGGGGCTGAATATGATGATATTGAGATCATAATTCATCCACAATCTATCATACATTCTATGGTCGAAA

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 8
lower sequence: EFJ07179 (Selaginella moellendorffii), 3'ss of exon 9
gtgtcatagagctccatcttttttgaaaaaaaaatctttaatccatatttattattaaacactaaattgacgacttggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA
                        | |||||||          ||| |||||  ||     || || | ||  |||   || | ||||  | || || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||| || || || || || || |||||||| ||| | || |
------------------------gtaaaaaaa----------catttttatacttgtctgctgaactaacatcttctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCCATTATACACTCCATGATCGAGA

upper sequence: GRMZM2G056975_T02 (Zea mays), 3'ss of exon 8
lower sequence: EFJ09183 (Selaginella moellendorffii), 3'ss of exon 9
gtgtcatagagctccatcttttttgaaaaaaaaatctttaatccatatttattattaaacactaaattgacgacttggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA
                        | |||||||          ||| |||||  ||     || || | ||  |||   || | ||||  | || || |||||||| || ||||| ||||| ||||| |||||||||||||| ||||| || || || || || || |||||||| ||| | || |
------------------------gtaaaaaaa----------catttttatacttgtctgctgaactaacatcttctgctggcagGGACTCGAGGTCATTGAAGCTCACTATTTGTTTGGAGCTGACTATGATGACATTGACATTGTTATCCATCCCCAATCGATTATACACTCCATGATCGAGA

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|14206809|gb|BG840487.1|BG840487
EST:     GGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACTTTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGAC
genomic: GGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACTTTATTCAACAAGgtgtcataga ... ggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGAC
EST: gi|211496438|gb|FL049443.1|FL049443
EST:     GGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACTTTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGA
genomic: GGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACTTTATTCAACAAGgtgtcataga ... ggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGA
EST: gi|32798103|gb|CD950339.1|CD950339
EST:     GGAATATGGGAAGGAAGATCACAGTAGATTCCGCTACTTTATTCAACAAG                         GGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGAC
genomic: GGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACTTTATTCAACAAGgtgtcataga ... ggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGAC

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), 48 (downstream exon)
Score: 24

TGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAAGCATCCAAACTGGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACTTTATTCAACAAGgtgtcataga ... ggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 586

TGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAAGCATCCAAACTGGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACTTTATTCAACAAGgtgtcataga ... ggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 482

TGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAAGCATCCAAACTGGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACTTTATTCAACAAGgtgtcataga ... ggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA


Block sizes: 40 (upstream exon), 48 (downstream exon)
Score: 15

TGACAGGCTGAAAGATGTAAAAGTTGCTGACGCTTTAAAGCATCCAAACTGGAATATGGGAAGGAAGATCACAGTAGATTCTGCTACTTTATTCAACAAGgtgtcataga ... ggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatctttaatccatatttattattaaacactaaattgacgacttggtcttgtagGGTTTAGAAGTTATTGAAGCACATTATTTATTTGGTGCTGAATATGATGACATTGAGATTGTGATTCACCCACAGTCTATCATACACTCTATGGTTGAAA
     tttaatccatatttat  TA-rich tract