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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcactgttataggggaaatatatatatatttctgcatgttcacctcttgcctcaccttgtgcctcaatcaaatcacttaaaagttttgtggcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGACAATTTAAATGTGGCCAAGGTTGCCGGGTTTATCAGATCAAAATCATGT

Basic information

species Zea mays
transcript GRMZM2G416069_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G416069_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA10G04300.2 (Glycine max), 3'ss of exon 18
------------------------------------------------------------------------------------------gcactgttataggggaaatatatatatatttctgcatgttcacctcttgcctcaccttgtgcctcaatcaaatcacttaaaagttttgtggcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGACAATTTAAATGTGGCCAAGGTTGCCGGGTTTATCAGATCAAAATCATGT
                                                                                          ||| | | |  |    |    | |||    |     | ||   ||  |  || | ||| |   || || ||     ||      ||  |     ||||||||  | ||| || ||||| || |||||||||||||| ||||||||  ||||||| || ||||| ||||||||||| || |||||  | |||||||| |||
gtaggagttgtttgtactactacttggattagaacaagaatattttataactactctgaatttgtgttttaataacaaaaattcatctaagcaatat-actgacacatctcacataagcctaaaactattttgctgatatcttatcttcttgttccattaatatggttccctacttacttcttgtttcagTTACAAGCCTTCCCCGTTTTTTATATTGGACGAAGTTGATGCTGCGTTGGACAACTTGAATGTTGCCAAGGTTGCTGGCTTTATTCGTTCAAAATCTTGT

upper sequence: GRMZM2G416069_T02 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G18470.1 (Glycine max), 3'ss of exon 17
------------------------------------------------------------------------gca-ctgttataggggaaatatatatatatttctgca--tgttcacctcttgcctcaccttgtgcctcaatcaaatcacttaaaagttttgtggcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGACAATTTAAATGTGGCCAAGGTTGCCGGGTTTATCAGATCAAAATCATGT
                                                                         || ||  ||||  |  |      | |||   ||  |  | ||   ||  |  || | |||     || || ||     ||      ||  |     |||||||| || ||| ||||| ||||| |||||||||||||| ||||||||  ||||||| || ||||| ||||||||||| || |||||  | |||||||| |||
gtagttgtttgtactaatattagaacaagaatattttgtaactactctgaatttgtgtttaataacacaaattcatctaatatactgacacatctcacataagcctaaaactattttgctgatatctgatcttcatgttccattaacatggttccctacttgcttcttgtttcagTTATAAGCCTTCACCATTCTTTATATTGGACGAAGTTGATGCTGCATTGGACAACTTGAATGTTGCCAAGGTTGCTGGCTTTATTCGTTCAAAATCTTGT

upper sequence: GRMZM2G416069_T02 (Zea mays), 3'ss of exon 8
lower sequence: Vv07s0005g03440.t01 (Vitis vinifera), 3'ss of exon 11
-----gcactgttataggggaaatatatatatatttctgcatgttcacctcttgcctcaccttgtgcctcaatcaaatcacttaaaagttttgtggcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGACAATTTAAATGTGGCCAAGGTTGCCGGGTTTATCAGATCAAAATCATGT
        || ||       ||| |    |    || || || | ||    |||  | ||    |      ||   || | ||  |  |     ||   |||||||| |||||| || || || || |||||||| ||||| ||||||||  |||||||| | ||||| || |||||||| || || ||| ||||||||||||||
tatatttccttttgccttcaaaaaaagattgctcttttg-atctgcaaaagttgaataactggctaataggatt--attattttta--tccatgggtggtttcagTTATAGGCCTTCTCCTTTTTTTATATTGGATGAAGTCGATGCTGCATTGGACAATCTGAATGTTGCTAAGGTTGCTGGATTCATCCGATCAAAATCATGT

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|67017957|gb|CO446706.1|CO446706
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|18659884|gb|BM500573.1|BM500573
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|60353637|gb|DN220610.1|DN220610
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|60399460|gb|DN232272.1|DN232272
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|5607711|gb|AI901378.1|AI901378
EST:     GCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|211099838|gb|FL388151.1|FL388151
EST:     GACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|60394410|gb|DN227280.1|DN227280
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|60349116|gb|DN216089.1|DN216089
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|9953703|gb|BE640286.1|BE640286
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|60396930|gb|DN229749.1|DN229749
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|32931521|gb|CF036333.1|CF036333
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|60340169|gb|DN207142.1|DN207142
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|32932198|gb|CF037010.1|CF037010
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|32839032|gb|CD978713.1|CD978713
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|60397605|gb|DN230421.1|DN230421
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|67026121|gb|CO454870.1|CO454870
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|211089791|gb|FL379369.1|FL379369
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|74034784|gb|DT535275.1|DT535275
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|60348508|gb|DN215481.1|DN215481
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|5895740|gb|AW036986.1|AW036986
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|32838704|gb|CD978385.1|CD978385
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|6742487|gb|AW313302.1|AW313302
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|211438053|gb|FL453415.1|FL453415
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|211072011|gb|FL419961.1|FL419961
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|60348556|gb|DN215529.1|DN215529
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTCTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
EST: gi|4680907|gb|AI629577.1|AI629577
EST:     GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAG                         TTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA
genomic: GGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGA

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), 49 (downstream exon)
Score: 543

ACACAGCTATGCCACCTACCAAGCGGTTTAGAGATATGGAACAGTTATCCGGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGACAATTTAAATGTGGCCAAGGTTGCCGGGTTTATCAGATCAAAATCATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

ACACAGCTATGCCACCTACCAAGCGGTTTAGAGATATGGAACAGTTATCCGGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGACAATTTAAATGTGGCCAAGGTTGCCGGGTTTATCAGATCAAAATCATGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 377

ACACAGCTATGCCACCTACCAAGCGGTTTAGAGATATGGAACAGTTATCCGGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGACAATTTAAATGTGGCCAAGGTTGCCGGGTTTATCAGATCAAAATCATGT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 235

ACACAGCTATGCCACCTACCAAGCGGTTTAGAGATATGGAACAGTTATCCGGTGGGGAGAAGACTGTTGCAGCACTGGCTTTGCTTTTTGCCATTCACAGgtaaaatgtt ... gcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGACAATTTAAATGTGGCCAAGGTTGCCGGGTTTATCAGATCAAAATCATGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcctcaccttgtgcctcaatcaaatcacttaaaagttttgtggcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGACAATTTAAATGTGGCCAAGGTTGCCGGGTTTATCAGATCAAAATCATGT
   gcctcac  putative branch site (score: 235)
                               ttaaaagtttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcactgttataggggaaatatatatatatttctgcatgttcacctcttgcctcaccttgtgcctcaatcaaatcacttaaaagttttgtggcaatttcagTTTTAGGCCATCACCGTTCTTCATATTGGACGAAGTAGATGCTGCTCTGGACAATTTAAATGTGGCCAAGGTTGCCGGGTTTATCAGATCAAAATCATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
gcactgt
- - - - - - - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaa