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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattttattcttattgctgtgagtttgctgatctatttttttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG

Basic information

species Zea mays
transcript GRMZM2G107867_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g17980.2 (Oryza sativa), 3'ss of exon 4
gtattttattcttattgctgtgagtttgctgatctatttttttttcctttttagaacaccatgtttcttgatac-atagtg--agtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
|| |||| || || ||  |||     ||  |  |||| | || || ||  || | |  | || ||| ||  ||  |||||   |  |||| ||||||||| || ||||||||| ||||||||||||||||||| ||||||||||| ||||| ||||| ||||||||||| |||||||| |||||||||||||||||||
gttttttttttttttt-ttgtatcactgtgggactatatcttcttgctcctttgcatgcaatattttttcttattatagtattatggttcctttgcagGTGATCTCTGGTAAATTATATGCTGGACCTGAGGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGATG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g37800.1 (Oryza sativa), 3'ss of exon 4
gtattttattcttattgctgtgagtttgctgatctatttttttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
||||||| ||  |||  |||||||  |    ||||   | ||  ||||||  |    |   | ||||||  || |   | |  || | ||||||||| || ||||||||| ||||||||||||| ||||| ||||||||||| ||||| ||||| ||||||||||| |||||||| ||||||||||||||||| |
gtattttttttgtatcactgtgagactat--atct---tcttgctcctttacatgcaatattttttcttattatagtattatggtccctttgcagGTGATCTCTGGTAAATTATATGCTGGACCCGAGGTTGATGTATGGAGCTGTGGAGTGATCCTTTATGCTCTCCTTTGTGGTACTCTTCCATTTGATGACG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 4
------------------------------gtattttattcttattgctgtgagt-ttgctgatctatttttttttcct---ttttaga---acaccatgtttcttgatacatagtgagtgt-------tcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
                              | || ||||| ||| || | | | | ||  |  | |||   |  |||      |||| |   ||  | |  |  || ||| ||   |  |         | |||  ||||| || ||||| ||| | ||||||||||| || || ||||| ||||| ||||| || ||| | ||||||||||| ||||| |||||||| ||||||||||
gtttgtaaataattaaattgtaacggaataggatattattattaatgttattattattattattatatcactacttctgagactttacatttacctccttgtgattaataaatcaaggataaactgttgtttttcacagGTTATCTCTGGAAAATTGTATGCTGGACCAGAAGTAGATGTCTGGAGCTGTGGTGTAATTTTATATGCTCTTCTCTGTGGCACTCTTCCTTTTGATGATG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 5
gtattttattcttattgctgtgagtttgctgatctatttttttttcctttttagaacac-catgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
        ||  || ||   |          |  |||| ||       | |  |        ||| ||||| |  | | |   |  | |||  ||||| || ||||| ||| | |||||||||||||| || ||||| ||||| ||||| || ||| | ||||| ||||||||||| || ||||| ||||||||||
-------gtttgtaatggaatacacggcaacaattattgttgaggatatatatgtgtgtgtgtgtgtcttggt-tacactttttcatttttcacagGTTATCTCTGGGAAATTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCCCTTCTTTGTGGCACCCTTCCTTTTGATGATG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 4
----gtattttattcttattgctgtgagt-ttgctgatc-tatttttttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
    ||| |  | |   || ||    | | ||| |||   ||| | | | |  | | | |     ||| ||||||| |  | | |   |  | |||  ||||| || ||||| ||||| |||||||||||||| || ||||| ||||| ||||| || ||| | ||||| ||||||||||| |||||||| ||||||||||
gtttgtaatggaatac-atggcgaaaattattgttgaggatatatatatattgtctcttgtgattcatatttcttggt-tacactttttcatttttcacagGTTATCTCTGGGAAACTGTATGCTGGACCTGAAGTGGATGTCTGGAGCTGTGGTGTAATTTTATATGCGCTTCTTTGTGGCACTCTTCCTTTTGATGATG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 4
gtattttattcttattgctgtgagtttgctgatctatttttttttcctttttagaacaccatgtttc--ttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
|||  |  |||      | |  |  |     ||    |  ||   | | |||  ||    | |||    | || |  ||   | ||||      |||||||| || || ||  |||||||||| ||||| || ||||| ||||| ||||| ||||| || || |||||||| ||||| || ||||||||||||||||
gtaagtgcttcagccctcaggtatctgaggaatactataattaggcttgtttcaaatgataggttatagtcgagatctataaattgttt-----cagGTAATTTCGGGCAAGTTATATGCTGGCCCTGAAGTAGATGTCTGGAGCTGTGGTGTGATACTCTACGCTCTTCTCTGTGGGACGCTTCCATTTGATGATG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: AT3G29160.2 (Arabidopsis thaliana), 3'ss of exon 4
----gtattttattcttattgctgtgagtttgctgatctattt--ttttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
     || |||| |    || |||     ||  | | |||| |   | | ||   |||     |  | || ||||    | || |     |  | ||| |||| ||||| |||||| |||||||||||||||| || |||||||||||||| || || ||  | || |||||  | || || |||||||| ||||||||||
gtatatagtttagtaaagttactgaattgtttttcacctatgtgactatgtctcgtttctcttatga-gtgtcttatctcttact-----tcttgttgtagGTTATATCAGGTAAATTATATGCTGGACCTGAAGTAGATGTATGGAGTTGCGGAGTTATATTGTACGCTCTATTATGCGGTACTCTTCCTTTTGATGATG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0040g00720.t01 (Vitis vinifera), 3'ss of exon 5
gtattttattcttattgctgtgagtttgctg-atctatttttttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
            ||| |  || |  ||| |  ||   ||     |    || |  |  |  ||| |   || ||||  |  |   | ||| ||||||| || ||||   |||||||| |||| |||||||| ||||| ||||||||||| || ||| | | ||||||||| |||||||  ||||| ||||||| ||
-----------gtatgg--gtcaacttgttatataagttgccaatgaacttgtgaataattatgctctgtg-tacaatgaaatactgcttgtgcagGTTATTTCTGAACAACTATATTCTGGTCCTGAGGTTGATGTTTGGAGTTGTGGTGTCATTTTATTTGCTCTTCTCTGTGGAAGGCTTCCTTTTGATGCTG

upper sequence: GRMZM2G107867_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------------gtattttattcttattg-ctgtgagtttgctgatctatttttttttcctttttagaacacc-----atgtttcttgatacatagtgagtgttc--ttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
                               | ||  |  || |||  || ||| |   | | | ||  ||| |    | | |  | |       |  |||||       || | ||||| |  ||||  |||| |||||||| | | | || || ||||||||||| ||||||||||| || || || ||| | || |||||||||||||| |||||||||||||||||||
gtaaggagtttgcagcattataatataagacaattcctaatttttggttgagagatgagtta-caatactttctaatatatgatgataatggttgaaatttctaaggttctaattagtgtcccattttatagGTTATATCTGGAAGATTGTACGCAGGACCTGAGGTGGATGTATGGAGCTGCGGTGTTATTTTGTACGCTCTTCTTTGTGGTACTCTTCCATTTGATGATG

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|71437399|gb|DR818449.1|DR818449
EST:     GCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAG                         GTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGT
genomic: GCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAGgtattttatt ... tcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGT
EST: gi|60359581|gb|DN226554.1|DN226554
EST:     GCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAG                         GTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGT
genomic: GCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAGgtattttatt ... tcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGT
EST: gi|71447675|gb|DR828725.1|DR828725
EST:     GCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAG                         GTAATATCTGGTAAACTATATGCTGGACCTGANGTCGATGTATGGAGTTGT
genomic: GCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAGgtattttatt ... tcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGT
EST: gi|211440538|gb|FL230375.1|FL230375
EST:     GCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAG                         GTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGC
genomic: GCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAGgtattttatt ... tcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGT

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: 45 (upstream exon), 45 (downstream exon)
Score: 91

GTATAATGTAAAACTTGCGGATTTTGGTCTGAGCAATGTCATGCATGATGGCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAGgtattttatt ... tcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 104

GTATAATGTAAAACTTGCGGATTTTGGTCTGAGCAATGTCATGCATGATGGCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAGgtattttatt ... tcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 177

GTATAATGTAAAACTTGCGGATTTTGGTCTGAGCAATGTCATGCATGATGGCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAGgtattttatt ... tcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 136

GTATAATGTAAAACTTGCGGATTTTGGTCTGAGCAATGTCATGCATGATGGCCATTTTCTGAAGACTAGCTGTGGGAGTCCGAACTATGCTGCTCCAGAGgtattttatt ... tcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttcctttttagaacaccatgtttcttgatacatagtgagtgttcttttgcagGTAATATCTGGTAAACTATATGCTGGACCTGAGGTCGATGTATGGAGTTGTGGGGTGATTCTTTATGCTCTTCTTTGTGGAACTCTTCCATTTGATGATG
                         tcttgat  putative branch site (score: 136)
                                          tgttctttt  putative PPT
       tttttagaa  TA-rich tract