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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataaaatatggaagttaaacttaattgtttacatggtgtggctgaagtttcctctttttcttttttttcccttatcttgtttactttctcaatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG

Basic information

species Zea mays
transcript GRMZM2G067985_T04
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g01600.2 (Oryza sativa), 3'ss of exon 3
aataaaatatggaagtta-aacttaattgtttacatggtgtggctgaagtttcctctttttcttttttttcccttatcttg-------tttactttctcaatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG
        | |  |  |   ||   ||||| | || |      |  |    |     |   |   |   |   |||| | |       | |  ||      ||| |||||||||| || || |||||||||||||| |||||||| ||||||||||| ||||||||||| ||||||||||||||||| ||||||||||| ||||||||
--------aagctacctgcgaccccattgtgtccaggcctgaacaaacagctaactgtcgacaagtaaatgttttatttagaggagcttatgtttctctgctctgcagGTATTGTTCTTGATTCTGGTGATGGTGTCAGCCACACAGTGCCCATTTATGAAGGATATGCGCTTCCTCATGCCATTCTCCGTTTGGATCTGGCTGGTCG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G05570.1 (Glycine max), 3'ss of exon 3
---aataaaatatggaagttaaacttaattgtttacatggtgtggctgaagtttcctctttttcttttttttcccttatcttgtttactttctcaatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG
       |  ||    |||   |  ||  ||  |   |    |   |       |  | || | |  || ||   || ||||||| |  ||   | |  ||||||||||| || || ||||||||||||||||||||||| |||||||| || ||||| ||||| ||||||||||| |||||||| ||||| |||||||| ||
attccacacgtacaagagtgggatatacatgcatttctacattaattatga--ccagcattatttccttattggtttgtcttgtt-atgttggtattaaacagGTATTGTGCTTGATTCTGGTGATGGTGTGAGCCACACGGTGCCCATATATGAAGGGTATGCTCTTCCTCATGCAATTCTTCGGTTGGACCTTGCTGGCCG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 3
aataaaatatggaagttaaacttaattgtttacatggtgtggctgaagtttcctctttttcttttttttcccttatcttgtttactttctcaatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG
|   | | |||   |  | |   |  | ||| ||   |    |   |    |    || | |  || ||  ||| ||||  |||  ||  || |  ||||||||||| || || ||||||||||||||||||||||| || ||||| || ||||| ||||| ||||||||||| |||||||| ||||| |||||||| ||
acatatacatgagtgggatatacatgtatttccacattaattcctcacgaccagtattatttccttattttcttgtctttgttatgttggcattaaacagGTATTGTGCTTGATTCTGGTGATGGTGTGAGCCACACAGTTCCCATATATGAAGGGTATGCTCTTCCTCATGCAATTCTTCGGTTGGACCTTGCTGGCCG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G15480.1 (Glycine max), 3'ss of exon 3
aataaaatatggaagttaaacttaattgttta-catggtgtggctgaagt--ttcctctttttcttttttttcccttatcttgtttactttctcaatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG
                         |||| || ||   | || ||  | |  ||| | | |       || | | ||  ||   | | || ||      |||||||||||| | |||||||||||||||||||| |||||||| || || || || || ||||| || || |||||||| |||||||||||||| ||||||||
-----------------------gtttgtatatcaccatctgtcttgattcattcttttataatcacattgttctttccctgaatcaattccttttaaaacagGTATTGTATTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCTGGTCG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 2
aataaaatatggaagttaaacttaattgtttacatggtgtggctgaagtttcctctttttcttttttttcccttatcttgtttactttctcaatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG
               ||  |  | |   | |   | |  |   |    |||  |  |    |  || || || |   |   || |||||  ||    ||||||||||  | |||||||||||||||||||| |||||||| || || || || || ||||| || || |||||||| |||||||||||||| || |||||
-------------gtttgtatattaccatctgtcttgattcattc---ttttataatcacatcattctttccctgaatcaattcctttcaaaa----cagGTATTGTGTTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCAGGTCG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 3
aataaaatatggaagttaaacttaattgtttacatggtgtggctga-agtttcctctttttcttttttttcccttatcttgtttactttctcaatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG
               ||  | ||   | |  |  || |     | | |||||  || |    || || || || |   |    |||||||| ||   |||||||||||  | |||||||| |||||||| || ||||||||||| || || || || ||||| || |||||||||||||||||||||||||||||||| ||
-------------gtttgtatttg--tatccatctgtttcaattcatagttttgtcatcacattgttctttccctgaatcaaatactttctgaa---acagGTATTGTTTTGGACTCTGGCGATGGTGTTAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTTCGTTTGGATCTTGCTGGCCG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 3
aataaaatatggaagttaaacttaattgtttacatggtgtggctgaagtttcctctttttcttttttttcccttatctt---gtttactttctcaatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG
                      || || ||| ||   | || || || |  |  |||| ||||    ||    |||| |    |  | | | |     | ||||||||||  | |||||||||||||||||||| ||||||||||| || || || || ||||| || |||||||||||||| ||||||||||||||||| ||
-----------------gtttgtacttatttcca---tctgtcttaattcactcctttgtcttcacattgttctatccttgaatcaaatctttttgaat-cagGTATTGTTTTGGACTCTGGTGATGGTGTGAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTCCGTTTGGATCTTGCTGGCCG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 3
lower sequence: AT3G18780.1 (Arabidopsis thaliana), 3'ss of exon 2
aataaaatatggaagttaaacttaattgtttacatggtgtggctgaagtttcctctttttcttttttttcccttatct-tgtttactttctcaatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG
                     ||| |   ||  | | | |   ||    | |   ||  || || |||   || | || || |||  ||| || |  ||||||||||| || || |||||||||||||||   ||||||||||| || ||||| || |   | |||||||||||||| || ||| | || |||||||| ||
--------------------gttagtacattttaggcttt--ttgtttatactcattgatcattatttgaactgagctctgattatcttc-cattgaacagGTATTGTGCTGGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACGAGGGTTTCTCTCTTCCTCATGCCATCCTCCGTCTTGACCTTGCTGGACG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 3
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 3
aataaaatatggaagttaaacttaattgtttacatggtgtggctgaagtttcctctttttcttttttttcccttatcttgtttactttctcaatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG
         | |   ||||   |||   |  |    || ||  | |  ||  || | || ||| | ||| | | |  | |||  |||| |  |   ||||||||||| ||||| |||||||||||||||   ||||||||||| || ||||| || ||||| ||||||||||| || |||||| | |||||||| |||||
-------gttagttcttaactctaaacatcca---agtctgagttatattatct-tcttacttgtatttacttaaagtcgttctctttttgta---acagGTATTGTGCTCGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACGAGGGGTATGCTCTTCCTCATGCTATCCTTCGTCTTGATCTTGCGGGTCG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 4
aataaaatatggaagttaaacttaattgtttacatggtgtggctgaagtttcctctttttcttttttttcccttatcttgtttactttctcaatctac-agGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG
         |     ||||| |    | |||  || |      | |  |||| | | | |  ||  | |  | |   ||  | |||| |||  |  || ||||||||| || || ||||||||||||||||| ||||||||||| ||||| ||||| ||||| ||||| ||||| || |||||| | || |||||||| ||
--------gttcgtattaaaat---ctttttggattggaattttcatttttcttttctgttgttagtgtagcctgagtt-ctaacttgctcctttgactagGTATTGTGCTGGATTCTGGTGATGGTGTGAGTCACACTGTGCCAATTTATGAAGGTTATGCACTTCCCCATGCTATCCTTCGTCTTGACCTTGCTGGACG

upper sequence: GRMZM2G067985_T13 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 3'ss of exon 2
aataaaatatggaagttaaacttaattgtttacatggtgtggctgaagtttcctctttttcttttttttcccttatcttgtttactttctcaatctac----agGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG
   ||  |   ||| ||   | | | | ||   |      | ||    |||  |||| | || || |||    ||| |  |  | ||| |   | |      |||||||||  | || |||||||||||||| ||||| || ||||| || || ||||||||||| ||||| ||||| || ||||| || || |||||||||||
--aaatttcaagaattttttcctcagtattggtaactgccgactatgattt--tcttatcctgttctttgttatatttactgaagttttttggtgtgtgaaaagGTATTGTCTTGGATTCTGGTGATGGTGTCAGCCATACAGTGCCAATCTATGAAGGATATGCTCTTCCACATGCAATCCTTCGATTAGACCTTGCTGGTCG

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|61117779|gb|DN558740.1|DN558740
EST:     TGTTGCAATCCAAGCGGTGCTCTCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|67028438|gb|CO457187.1|CO457187
EST:     TGTTGCAATCCAAGCGGTGCTCTCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTACTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|61117780|gb|DN558741.1|DN558741
EST:     TGTTGCAATCCAAGCGGTGCTCTCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|22542171|gb|BU092609.1|BU092609
EST:     GCAATCCAAGC-GGGCTCTCACTTTATGCTAG-GGGCGTACTACTG                         GTATTGTACTCGACTCTGG-GATGG-GTGAGCCACACTGTGCCCATTTACG
genomic: GCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|31350149|gb|CD434506.1|CD434506
EST:     TGTTGCAATCCAAGCGGTGCTCTCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|31250096|gb|CD219120.1|CD219120
EST:     TGTTGCAATCCAAGCGGTGCTCTCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|211466787|gb|FL184427.1|FL184427
EST:     TGTTGCAATCCAAGCGGTGCTCTCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|211469308|gb|FL184436.1|FL184436
EST:     TCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
genomic: TCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|13490635|gb|BG517399.1|BG517399
EST:     TGTTGCAATCCAAGCGGTGCTCTCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTACTCGACTCTGGTGATGGTGTGAGTCTCACACTGTGCCCATTTA
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAG-C-CACACTGTGCCCATTTA
EST: gi|211469316|gb|FL184444.1|FL184444
EST:     TGTTGCAATCCAAGCGGTGCTCTCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|60345925|gb|DN212898.1|DN212898
EST:     AGTGGGCGTACTACTG                         GTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
genomic: AGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|32862856|gb|CF002538.1|CF002538
EST:     TGTTGCAATCCAAGCGGTGCTCTCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|31355571|gb|CD439928.1|CD439928
EST:     TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTTCTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|5928698|gb|AW055915.1|AW055915
EST:     TGTTGCAATCCAAGCGGTGCTCTCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTACTCGACTCTGGTGATGGNGTGAGCCACACTGTGCCCATTTACG
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
EST: gi|211466785|gb|FL184425.1|FL184425
EST:     TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTG                         GTATTGTTCTTGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG
genomic: TGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACG

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), 46 (downstream exon)
Score: 128

GAGAAGATGACCCAAATTATGTTTGAGACTTTCAATGTTCCTGCCATGTATGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

GAGAAGATGACCCAAATTATGTTTGAGACTTTCAATGTTCCTGCCATGTATGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 86

GAGAAGATGACCCAAATTATGTTTGAGACTTTCAATGTTCCTGCCATGTATGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 96

GAGAAGATGACCCAAATTATGTTTGAGACTTTCAATGTTCCTGCCATGTATGTTGCAATCCAAGCAGTTCTATCACTCTATGCTAGTGGGCGTACTACTGgtatgacctg ... caatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttcctctttttcttttttttcccttatcttgtttactttctcaatctacagGTATTGTACTCGACTCTGGTGATGGTGTGAGCCACACTGTGCCCATTTACGAAGGATATGCCCTTCCTCATGCCATTCTTCGTTTGGATCTTGCTGGTCG
       ctctttttcttttttt  CT-rich tract
        tctttttctttttttt  TA-rich tract