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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgactcgttcacatggcgaccaaatttcattaggacttacaaattttcccatcttaattatgggttgctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG

Basic information

species Zea mays
transcript GRMZM2G006765_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os11g06390.6 (Oryza sativa), 3'ss of exon 3
gtaatgactcgttcacatggcgaccaaatttcattaggacttacaaattttcccatcttaattatgggttgctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
||||| ||||  ||||||||             | ||   ||  |||  |   ||  ||| | |||   || || || | || ||||||| || ||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||| || ||||||||||||||
gtaataactcactcacatggt------------tgagagttttaaaaaatattcactttattcatgaactgttgctcttgatgcagGTATCGTGTTGGACTCTGGTGATGGTGTCAGCCACACCGTGCCAATCTATGAAGGATATGCCCTTCCTCATGCCATCCTGCGTCTGGACCTTGCTGGGCG

upper sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G05570.1 (Glycine max), 3'ss of exon 3
---------gta-atgactcg--ttcacatggcgaccaaatttcattaggacttacaa-attttcccatc--ttaattatgggttgctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
         ||| | || | |  |  |||||     | |  || |||| |||   ||  |||| |  ||   ||  |  ||   || || | || |  ||||||||||  | || |||||||||||||| |||||||| ||||| || |||||||| ||||| ||||||||||| || || ||  | ||||||||||| ||
attccacacgtacaagagtgggatatacatgcatttctacattaattatgaccagcattatttccttattggtttgtcttgttatgttggt-attaaacagGTATTGTGCTTGATTCTGGTGATGGTGTGAGCCACACGGTGCCCATATATGAAGGGTATGCTCTTCCTCATGCAATTCTTCGGTTGGACCTTGCTGGCCG

upper sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 3
------------gtaatgactcgttcacatggcgaccaaatttcattaggacttacaa-attttcccat---cttaattatgggttgctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
            ||   ||         ||  | ||   | ||| | | |||    |  |||| |  ||   |||   | ||   || ||  ||| |  ||||||||||  | || |||||||||||||| ||||||||||| || || |||||||| ||||| ||||||||||| || || ||  | ||||||||||| ||
acatatacatgagtgg-gatatacatgtatttccacattaattcctcacgaccagtattatttccttattttcttgtctttgttatgttgg-cattaaacagGTATTGTGCTTGATTCTGGTGATGGTGTGAGCCACACAGTTCCCATATATGAAGGGTATGCTCTTCCTCATGCAATTCTTCGGTTGGACCTTGCTGGCCG

upper sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G15480.1 (Glycine max), 3'ss of exon 3
gtaatgactcgttcacatggcgaccaaatttcattaggacttaca-aattttcccatcttaattatgggttg-ctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
        | ||  | ||  | | |    || |||    |||  | |||       |  |     ||  |    |  |  | |  ||||||||||||||||||||||||||||||| || ||||| || ||||||||||| || ||||| || || ||||||||||| ||  | || || ||||| ||
------gtttgt--atatcaccatctgtcttgattcattcttttataatcacattgttctttccctgaatcaattccttttaaaacagGTATTGTATTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCTGGTCG

upper sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 2
gtaatgactcgttcacatggcgaccaaatttcattaggacttaca-aattttcccatcttaattatgggttgctgttcatcatt-cagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
        | ||  | ||  | | |    || |||    |||  | |||     |||  |     ||  |   |     |||   |||||||||| |||||||||||||||||||| || ||||| || ||||||||||| || ||||| || || ||||||||||| ||  | || || || || ||
------gtttgt--atattaccatctgtcttgattcattcttttataatcacatcattctttccctgaatcaattcctttcaaaacagGTATTGTGTTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCAGGTCG

upper sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 3
gtaatgactcgttcacatggcgaccaaatttcattaggacttacaaattttcccatcttaattatgggttgctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
||    | | ||   |||      ||| |   | |        || ||| | |  ||      ||    | || |     |  |||||||||| ||||||||||| |||||||| || ||||| |||||||||||||| || ||||| || ||||||||||| || ||  | || |||||||| ||
gtttgtatttgtatccatctgtttcaattcatagttttgtcatcacattgttctttccctga-atcaaatactttctgaaa--cagGTATTGTTTTGGACTCTGGCGATGGTGTTAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTTCGTTTGGATCTTGCTGGCCG

upper sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 3
gtaatgactcgttcacatggcgaccaaatttcattaggacttacaaattttcccatcttaattatgggttgctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
||    |||  ||  |||       || |  |         | || ||| | | ||| |         |     ||  | | ||||||||||| |||||||||||||||||||| || ||||| |||||||||||||| || ||||| || ||||||||||| || ||  | || |||||||| ||
gtttgtacttatttccatctgtcttaattcactcctttgtcttcacattgttctatccttgaatcaaatc----tttttgaatcagGTATTGTTTTGGACTCTGGTGATGGTGTGAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTCCGTTTGGATCTTGCTGGCCG

upper sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT3G18780.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaatgactcgttcacatggcgaccaaatttcattaggacttacaaat--tttcccatcttaattatgggttgctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
          |||   |           |||  ||   ||| |   ||  ||        | |     | ||    | |||    ||||||||||  |||| ||||||||||||||    ||||| ||||||||||| || ||||   | ||||||||||||||||| || |||||||||||||| ||
----------gttagtacattttaggctttttgtttatactcattgatcattatttgaactgagctctgattatcttccattgaacagGTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACGAGGGTTTCTCTCTTCCTCATGCCATCCTCCGTCTTGACCTTGCTGGACG

upper sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaatgactcgttcacatggcgaccaaatttcattaggacttacaaattttcccatcttaattatgggttgctgttcatcatt--cagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
|| |   ||       |   |  |||| | | | |   | |||     || |   | || | |    || | | |   |   |  ||||||||||  | || ||||||||||||||    ||||| ||||||||||| || || ||||| ||||||||||| ||||| || ||||| ||||| || ||
gttagttcttaactcta-aacatccaagtctgagttata-ttatcttcttacttgtatttacttaaagtcgttctctttttgtaacagGTATTGTGCTCGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACGAGGGGTATGCTCTTCCTCATGCTATCCTTCGTCTTGATCTTGCGGGTCG

upper sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
lower sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 3
-----gtaatgact--cgttcacatggcgaccaaa-tttcatta---ggacttacaaattttcccatcttaattatgggttgctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
      | || | |   ||  | |    || |||| |||  ||    |   |||   ||| |  ||| || || |  |     || |  || || ||||||||| ||||||||||||||||||||    ||||| ||||| ||||| || ||||   | ||||| ||||| ||||| || || ||||||||||| ||
gttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatgattttc-tttagGTATTGTGTTGGACTCTGGTGATGGTGTGTCTCACACTGTGCCTATCTACGAGGGTTTCTCACTTCCACATGCTATCCTCCGTCTCGACCTTGCTGGTCG

upper sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 4
----gtaatgactcgttcacatggcgaccaaatttcattaggacttacaaattttcccat---cttaattatgggttgctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
    ||| | |    ||        |   || |||||||     || |   | ||    |   || | || |   |||||   | |     |||||||||  |||| |||||||||||||| || ||||| |||||||| |||||||||||||| ||||| ||||| ||||| || |||||||||||||| ||
gttcgtattaaaatctttttggattgg--aattttcatttttcttttctgttgttagtgtagcctgagttctaacttgct--cctttgactagGTATTGTGCTGGATTCTGGTGATGGTGTGAGTCACACTGTGCCAATTTATGAAGGTTATGCACTTCCCCATGCTATCCTTCGTCTTGACCTTGCTGGACG

upper sequence: GRMZM2G006765_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 3'ss of exon 2
-----gtaatgactcgttcac--atggcgaccaaatttcattaggacttacaaat-------tttcccatcttaattatgggttgctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
       ||  | |  |||     |   |   |      | || || || |  ||       |||   || || | |   | ||  || |        ||||||||| ||||| |||||||||||||||||||| |||||||||||||||||||| ||||| ||||| ||||| ||||| ||  | ||||||||||| ||
aaatttcaagaattttttcctcagtattggtaactgccgactatgattttcttatcctgttctttgttatatttactgaagttttttggtgtgtgaaaagGTATTGTCTTGGATTCTGGTGATGGTGTCAGCCATACAGTGCCAATCTATGAAGGATATGCTCTTCCACATGCAATCCTTCGATTAGACCTTGCTGGTCG

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|32868978|gb|CF008660.1|CF008660
EST:     TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTG                         GTATTGTATTGGACTCT
genomic: TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCT
EST: gi|78117775|gb|DV536162.1|DV536162
EST:     TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTG                         GTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
genomic: TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
EST: gi|71315363|gb|DR794285.1|DR794285
EST:     TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTG                         GTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
genomic: TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
EST: gi|32869665|gb|CF009347.1|CF009347
EST:     TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTG                         GTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
genomic: TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
EST: gi|6695747|gb|AW288825.1|AW288825
EST:     TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTG                         GTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
genomic: TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
EST: gi|32869014|gb|CF008696.1|CF008696
EST:     TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTG                         GTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
genomic: TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
EST: gi|32870978|gb|CF010660.1|CF010660
EST:     TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTG                         GTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
genomic: TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
EST: gi|101383600|gb|EB813855.1|EB813855
EST:     TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTG                         GTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
genomic: TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
EST: gi|60347189|gb|DN214162.1|DN214162
EST:     TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTG                         GTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
genomic: TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG
EST: gi|78179272|gb|DV549645.1|DV549645
EST:     TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTG                         GTATTGTATTGGACTCTGGTGATGGTGTCACCCACACAGTGCCAATCTATG
genomic: TGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATG

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), 47 (downstream exon)
Score: 34

GAGAAGATGACCCAAATCATGTTTGAGACTTTCAATGTTCCTGCCATGTATGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 28

GAGAAGATGACCCAAATCATGTTTGAGACTTTCAATGTTCCTGCCATGTATGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG


Block sizes: 48 (upstream exon), 35 (downstream exon)
Score: 11

GAGAAGATGACCCAAATCATGTTTGAGACTTTCAATGTTCCTGCCATGTATGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 173

GAGAAGATGACCCAAATCATGTTTGAGACTTTCAATGTTCCTGCCATGTATGTCGCCATCCAGGCTGTGCTTTCCCTGTACGCCAGTGGACGTACAACTGgtaatgactc ... catcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaggacttacaaattttcccatcttaattatgggttgctgttcatcattcagGTATTGTATTGGACTCTGGTGATGGTGTCAGCCACACAGTGCCAATCTATGAAGGTTATGCCCTTCCTCATGCCATCCTGCGCCTTGACCTTGCTGGGCG
         ttacaaatttt  TA-rich tract