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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaacaatactctttacttctttagagtgtttacattttgacttacatgtgcatatatgattgatctttctatttttattccag

Basic information

species Zea mays
transcript GRMZM2G340527_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 5'ss of exon 13
TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaacaatactctttacttctttagagtgtttacattttgacttacatgtgcatatatgattgatctt-tctatttttattccag
|||||||||||||||| ||||||||||||||||||||||||||||||||||| ||||||||||| || |||||||| || ||||| || ||||||||||||| |||||| | ||| ||  |||      |||| |     |      |||| |||| |||  ||||||| || | || || | ||||||
TTGTTGCTCCAATGCCTACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAATGCTTTGAACCTTATACATCTAACATATACAGCCGGCGGGTTCTAAGgtttgtaactacactgtt--ctt------agtgctcgtgctca---ctacaggtgcttat--gattgattttgtttaattcttttccag

upper sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA04G39500.1 (Glycine max), 5'ss of exon 13
TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaacaatactctt--tacttctttagagtgtttacattttgacttacatgtgcatatatgattgatctttctatttttattccag
| || || || ||||| ||||| |||||||| ||||||||||| || |||||||| |||||||| || || || ||||| ||||||||  | ||| |||||| ||        | | |  || |   |    |||| |  ||||    |  ||||  | ||| | ||||  |   || ||| | ||| ||
TCGTGGCCCCTATGCCAACTGCATCCACTAGCCAGATTCTTGGAAATAATGAGTGTTTTGAACCATATACTTCAAATATCTACAGTCGTAGAGTTTTAAGgtttgctttttcgcccgtgttattctgtcttggtgtat-tattt----tcccatgatcctatcttattgggcaa-ctgtttgt-ttctag

upper sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA08G15360.1 (Glycine max), 5'ss of exon 15
--------TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaacaatactct-ttacttctttagagtgtttacattttgacttacat-gtgcatatatgattgatctttctatttttattccag-------------
        ||||||| || ||||| ||||| || ||||| |||||||||||||| |||||||| ||||| || || || |||||||| ||||||||  | ||| |||||    |  |  |||  | ||| |  |||    | | |   | ||||  ||  | |    |  |   ||  ||||||  |  | | |                 
CTCACTTCTTGTTGCCCCTATGCCAACTGCATCAACTAGCCAGATTCTTGGCAATAATGAGTGTTTTGAGCCATATACTTCTAATATCTACAGTCGTAGAgttttaaggctcattgccgtaccatcttattattttttgatatct---tattgatctattttgattgttaactgtttgtctttcagtggtgaatttgttgtggtgaacaag

upper sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA05G32070.1 (Glycine max), 5'ss of exon 13
TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaacaatactctttacttctttagagtgtttacattttgacttacatgtgcatatatgattgatctttctatttttattccag
||||||| || ||||| ||||| || ||||| |||||||||||||| |||||||| ||||| || || || |||||||| ||||| ||  | |||||||||| | |  | |||    | |  |  |||   |||||  || |   ||||    |  || | ||||||   |  || ||| | || |||
TTGTTGCCCCTATGCCAACTGCATCAACTAGCCAGATTCTTGGCAATAATGAGTGTTTTGAGCCATATACTTCTAATATCTACAGCCGCAGAGTTCTAAGgtttattgccata----tcatcttatta---tgttttgatat---cttattgatctatct-tgattg--ttaactgtttgtctttcag

upper sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT2G21790.1 (Arabidopsis thaliana), 5'ss of exon 13
TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaacaatactctttacttctttagagtgtttacattttgacttacatg-tgcatatatgattgatctttctatttttattccag
| || || |||||||| |||||||| || ||||| || ||||| |||||||| || ||||| ||||||||||| || || ||||| ||  | ||  | |||| ||| |  ||     | | ||    ||  |||||    |||  |  |  || ||| ||     ||| |  |  |  |||   | |||
TAGTAGCACCAATGCCAACTGCTTCAACCAGTCAAATCCTTGGGAACAATGAATGTTTTGAGCCCTACACATCAAACATCTACAGCCGCAGAGTCTTGAGgtatgtgaatat-taaatcatttgacaagtatgtttctggttttccccatttgatgcttactcacttggttgtcttggttt--gtacag

upper sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 5'ss of exon 13
TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaacaatactctttacttctttagagtgtttacattttg-acttacatgtgcatatatgattgatctttc--tatttttattccag
|||| || || |||||||||||||| || || ||||||||||| ||||||||||||||||| ||||| || || ||||| |||||| |  | |||||||||| |||     ||| ||  || | || |   |  | | |||| | ||||   |   ||| || |  |  ||||||  | ||| | |  |||
TTGTAGCACCTATGCCCACTGCTTCAACCAGCCAGATTCTTGGAAACAATGAGTGCTTTGAGCCCTATACTTCCAATATCTACAGTAGGAGAGTTCTAAGgtttgttttgctacccta-acctgttcatttt-ctaagatttagtacttttgttgccatctaagtctcctctttccttgtttctttgtcag

upper sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 13
lower sequence: PP1S64_38V6.1 (Physcomitrella patens), 5'ss of exon 7
TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaacaatactctttacttctttagagtgtttacattttgacttacatgtgcatatatgattgatctttctatttttattccag
|  | || |||||||||||||| || || ||||| ||  | ||||||||||||||||| || || || ||||| || ||||||||  |||| || || ||||   |||    || |   || | |   || | ||  |       ||| | | |  || || ||   | |   || |  || | ||||
TCTTGGCACCAATGCCCACTGCATCGACCAGTCAAATCTTAGGCAACAATGAGTGCTTCGAGCCGTATACATCGAACATTTACAGCAGACGAGTACTGAGgtacttaa-gtcacgcccaacattt---gaattttcgctgaaaagctttcttatttatctaggaactaaccccctctggtt-tgccag

upper sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 13
lower sequence: EFJ14283 (Selaginella moellendorffii), 5'ss of exon 12
TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaacaatactctttacttctttagagtgtttacattttgacttacatgtgcatatatgattgatctttctatttttattccag
|||||||||||||||| || || || || || || |||||||| ||||| ||||| ||||| || || ||||| |||||||||| |||||| |||||||||| ||   |     ||| || |    |    |  |||  ||       |||                                     
TTGTTGCTCCAATGCCGACAGCATCAACAAGCCAAATTCTTGGAAACAACGAGTGTTTTGAGCCTTATACATCCAATATTTACACTCGACGCGTTCTAAGgtatgc--cttctttctgta-tcagctgtgatacttatgttgcctgccacag------------------------------------

upper sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 13
lower sequence: EFJ20162 (Selaginella moellendorffii), 5'ss of exon 1
TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaacaatactctttacttctttagagtgtttacattttgacttacatgtgcatatatgattgatctttctatttttattccag
|||||||||||||||| || || || || || || |||||||| ||||| ||||| ||||| || || ||||| |||||||||  |||||| |||||||||| ||   |     ||| || |    |    |  |||  ||      ||||                                     
TTGTTGCTCCAATGCCGACGGCATCAACAAGCCAAATTCTTGGAAACAACGAGTGTTTTGAGCCTTATACATCCAATATTTACGCTCGACGCGTTCTAAGgtatgc--cttctttctgta-tcagctgtgatacttatgttgcctgctacag------------------------------------

upper sequence: GRMZM2G340527_T01 (Zea mays), 5'ss of exon 13
lower sequence: EFJ20157 (Selaginella moellendorffii), 5'ss of exon 12
TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaacaatactctttacttctttagagtgtttacattttgacttacatgtgcatatatgattgatctttctatttttattccag
|||||||||||||||| || || || || || || |||||||| ||||| ||||| ||||| || || ||||| |||||||||| |||||| |||||||||| ||   |     ||| || |    |    |  |||  ||      ||||                                     
TTGTTGCTCCAATGCCGACAGCATCAACAAGCCAAATTCTTGGAAACAACGAGTGTTTTGAGCCTTATACATCCAATATTTACACTCGACGCGTTCTAAGgtatgc--cttctttctgta-tcagctgtgatacttatgttgcctgctacag------------------------------------

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|211165336|gb|FL103224.1|FL103224
EST:     GAGTGCTTTGAACCCTACACATCTAATATATACAGTCGACGGGTTCTAAG                         TGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
genomic: GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
EST: gi|21389965|gb|BQ528014.1|BQ528014
EST:     GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAG                         TGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
genomic: GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
EST: gi|76015090|gb|DT942260.1|DT942260
EST:     GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAG                         TGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
genomic: GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
EST: gi|211165337|gb|FL103225.1|FL103225
EST:     GAGTGCTTTGAACCCTACACATCTAATATATACAGTCGACGGGTTCTAAG                         TGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
genomic: GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
EST: gi|76018236|gb|DT945406.1|DT945406
EST:     GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAG                         TGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
genomic: GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
EST: gi|32930349|gb|CF035161.1|CF035161
EST:     GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAG                         TGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
genomic: GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
EST: gi|32932558|gb|CF037370.1|CF037370
EST:     GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAG                         TGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
genomic: GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
EST: gi|211165340|gb|FL103228.1|FL103228
EST:     GAGTGCTTTGAACCCTACACATCTAATATATACAGTCGACGGGTTCTAAG                         TGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
genomic: GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
EST: gi|32919054|gb|CF023866.1|CF023866
EST:     GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAG                         TGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT
genomic: GAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAAT

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), 45 (downstream exon)
Score: 316

TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAATGGGCATTTGGACTCCTACTCTGAAAAACCAGATAATATATGATGATGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAATGGGCATTTGGACTCCTACTCTGAAAAACCAGATAATATATGATGATGGT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 43

TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAATGGGCATTTGGACTCCTACTCTGAAAAACCAGATAATATATGATGATGGT


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 71

TTGTTGCTCCAATGCCCACTGCTTCCACTAGTCAGATTCTTGGCAACAATGAGTGCTTTGAACCCTACACATCTAATATTTACAGTCGACGGGTTCTAAGgtctgtaaca ... tttattccagTGGGGAATTTGTTGTGGTTAACAAGCATCTTCTTCATGATTTGACTGAAATGGGCATTTGGACTCCTACTCTGAAAAACCAGATAATATATGATGATGGT