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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttctttgtttttgtgagcaggatctactcaacatccacgctaagatttgtgccccactgtaaaactttagtaactgatgaatgttctgcacattactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG

Basic information

species Zea mays
transcript GRMZM2G017089_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 3'ss of exon 9
gtaagtttttctttgtttttgtgagcaggatctactcaacatcca--cgctaagatttgtgccccactgtaa-----aactttagtaactgatgaatgttctgcacattactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG
||| ||||||||| |  || || |  |||||||    | || ||   | ||   | ||||    | || |||     || || | | |||||| |||    ||  ||||    |||| |||||||| |||||||| ||||| ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||
gtacgtttttcttggcattggttattaggatctgtatagcagccttccactgctacttgttttactctataagttataagttcatttactgataaattcaatgtgcattg---tagGGCTTGCTGTGAGCCAACGGCACACATATTTATTTTCTGCTGGTGATGACAAACAAGTAAAGTGTTGGGATCTTGAACAAAACAAG

upper sequence: GRMZM2G017089_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA09G04910.1 (Glycine max), 3'ss of exon 8
gtaagtttttctttgtttttgtgagcaggatctactcaacatccacgctaagatttgtgccccactgtaaaactttagtaa-ctgatgaatgttctgcacattacta-tagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG
                                      |   ||| | ||  ||| |||       | ||   |  || |   | || |      || || ||  ||  ||| |||||||| ||| |  | || |||||  | || ||||||||||| || |||||||| |||||||||||||||||||| || |||
---------------------------------gtatgatg-ccaaggtattattggtggtg-gtagcaattgtgaagcaggttaataataacaatgtacttttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGACGATAAACAAGTTAAATGTTGGGATCTTGAACAGAATAAG

upper sequence: GRMZM2G017089_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA15G15960.2 (Glycine max), 3'ss of exon 7
gtaagtttttctttgtttttgtgagcaggatctactcaacatccacgctaagatttgtgccccactgtaaaactttagtaactgatgaatgttctgcacattactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG
                        | | |||      ||  |      ||    | ||  |  | ||| || |    || | | || ||   | |||   ||   | ||| |||||||| ||| |  | || |||||  | || |||||||||||||| |||||||| ||||||||||| |||||||| || |||
------------------------gtaagatgc---taaggtgt-tattagtggtggtagca-attgtgaacc--aggttaataat-aacaatgtgc-ttttttaacagGTCTTGCTGTTAGCAACAGACATACTTACATGTTCTCTGCTGGTGATGATAAACAAGTTAAATGTTGGGACCTTGAACAGAATAAG

upper sequence: GRMZM2G017089_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT3G16650.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtttttctttgtttttgtgagcaggatct--actcaacatccacgctaagatttgtgccccactgtaaaactttagtaactgatgaatgttctgca--cattact--atagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG
|| ||  |    || ||||      ||   | |    | | ||    | ||   |     |  ||| ||||||| |||   ||||    ||  || |  |   |||  |  | ||| || ||||| ||| |  | || || ||| | |||||||||||||||||||| ||||| ||||| ||||| ||||| || || |||
gttagactactatttttttccccctcaatttgttagtttatcaatagctcttgtagaaaagtaccagtgtaaaagttt--caactctctaagtttatataattattgtttcacagGCCTCGCTGTAAGCAATAGACATACCTATATGTTTTCTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAG

upper sequence: GRMZM2G017089_T02 (Zea mays), 3'ss of exon 7
lower sequence: AT4G15900.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaagtttttc---tttgtttttgtg-agcaggatctactcaacatccacgc---taagatttgtgccccactgtaaaactttagtaactgatgaatgttctgcacattactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG
|| ||  ||||   | |||| | ||  |  |  || |  |  || |         ||| | |   |   ||   || || ||| |   ||  |    ||| || |  ||  || ||| || ||||| ||| | || || || ||| | || ||||||||||||||||| ||||| ||||| ||||| ||||| || || |||
gttagcctttcaaatctgttctcgtttattaatatttgttagacttttcaataaataacactctcgggacaagttacaagtttgggctctttt----gttttgaattttgttacagGCCTCGCTGTAAGCAATCGACATACCTATATGTTCTCTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAG

upper sequence: GRMZM2G017089_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv05s0077g02310.t01 (Vitis vinifera), 3'ss of exon 8
gtaagtttttctttgtttttgtgagcaggatctactcaacatccacgctaagatttgtgccccactgtaaaactttagtaactgatga-atgttctgcacattactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG
                                   | |   |    |  |  |||| |      || ||    | |  |  || || | ||    ||   | |  |  ||| |||||||| ||| |    || || ||| | || || |||||||||||||||||||| ||||| ||||| |||||||| || |||
----------------------------------gttagt-ttattgtcataatttctattg-gctttat--ttctgctggctaatcatatacagtgtttact-ttgcagGCCTTGCTGTTAGCAACAAACATACATATATGTTCTCAGCTGGTGATGACAAACAAGTTAAATGCTGGGACCTTGAACAGAATAAG

upper sequence: GRMZM2G017089_T02 (Zea mays), 3'ss of exon 7
lower sequence: PP1S402_49V6.1 (Physcomitrella patens), 3'ss of exon 7
gtaagtttttctttgtttttgtgagcaggatctactcaacatccacgctaagatttgtgccccactgtaaaactttagtaactgatgaatgttctgcacattactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG
           ||||||  || |    ||    |  | |  |  || || || ||| |       ||  | |  ||   | |  |||||||      |     |   ||| ||||| || |||   || ||  |||||||||| || ||||||||||||||||| || |||||||||||||||||| | || |||
----------gtttgttactgagt-ttggccaaatcccatttttacacttag-tttctattgatgtggcacatgttgacagcaaatgaatggatgtgat----cggcagGCCTTGCAGTGAGCGCCCGGCATCCTTATTTATTCTCAGCTGGTGATGACAAACAGGTCAAATGTTGGGATCTTGAATACAATAAG

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|78085590|gb|DV513983.1|DV513983
EST:     ATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTG                         GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACA
genomic: ATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTGgtaagttttt ... attactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACA
EST: gi|6021220|gb|AW066148.1|AW066148
EST:     ATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTG                         GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACA
genomic: ATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTGgtaagttttt ... attactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACA
EST: gi|32933221|gb|CF038033.1|CF038033
EST:     ATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTG                         GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACA
genomic: ATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTGgtaagttttt ... attactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACA
EST: gi|211016045|gb|FL237689.1|FL237689
EST:     ACTGACTGGTCATATTGAGCAAATTCGTG                         GACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACA
genomic: ACTGACTGGTCATATTGAGCAAATTCGTGgtaagttttt ... attactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACA
EST: gi|148962621|gb|EE013511.2|EE013511
EST:     ATCAGGAACCCTGAAGCTTACACTGACTGGCCATATTGAGCAAATTCGTG                         GACTTGCTGTCAGCCAACGTCACACTTATTTATT
genomic: ATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTGgtaagttttt ... attactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATT

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), 48 (downstream exon)
Score: 624

ATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTGgtaagttttt ... attactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 341

ATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTGgtaagttttt ... attactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 369

ATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTGgtaagttttt ... attactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 365

ATATGGGATCTTGCATCAGGAACCCTGAAGCTTACACTGACTGGTCATATTGAGCAAATTCGTGgtaagttttt ... attactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgccccactgtaaaactttagtaactgatgaatgttctgcacattactatagGACTTGCTGTCAGCCAACGTCACACTTATTTATTTTCTGCTGGTGATGACAAACAAGTAAAATGTTGGGATCTTGAACAAAACAAG
             taaaactttagtaa  TA-rich tract