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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttgacctagcgggcaactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcag

Basic information

species Zea mays
transcript GRMZM2G052403_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 5'ss of exon 22
CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttgacctagcgggca-actgatgagattcact--------tgtg--tctcaagcctaaccagtggttcgtttactttcag
 ||||||||||| ||||||||||| |||||||| || |||||||||||||||||||||||||| ||||| || ||||||||||| |||||||| |||||||||| ||   | | |        | | ||||| |  ||         ||||  ||||||  ||||    || ||  | |||||||||
TGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATATCAATGTCAAGCATTACATCGAAGgtatgatggcatccaaattttgcattaatgaggtgtacagtgtactatgtgattctcaaagctaaatgctgttttttctactttcag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA10G02400.1 (Glycine max), 5'ss of exon 21
CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttgacctagcgggcaactgatgagattcactt------gtgtctcaagcctaaccag----tggttcgtttactttcag
 || || |||||||| || ||||| |||||||| || || |||||||||||||| || || |||||||| || || |||||||| |||||||| || ||||||||| |      ||        |  || | |  | ||       ||  |||     ||  |     |||||   ||  || |||
TGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTTCAATGTCCAGCATTACTTCAAAGgtattaatgttgtaagttacttttttttgtggtgtatttccttgtatgcttcagtgacaagaaaaatatggttttgtttgttgcag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA02G17400.1 (Glycine max), 5'ss of exon 18
CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg---acctag-cgggcaactgatgagattcacttgtgtctcaagc-ctaaccagtggttcgtttactttcag------
 || || |||||||| || ||||| |||||||| || || || ||||||||||| || || ||||| || || || |||||||| |||||||| || ||||||||| |||   |  ||  | |        |    |  | ||   | |||  |  |||      |    ||   |||  |      
TGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTTCAATGTCCAGCATTACATCCAAGgtattagttgcaaatttaaactgttttgctctactctgtattttcctttcattcattaagtgacaggatattgtttttttgttgcag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA02G17410.1 (Glycine max), 5'ss of exon 17
CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatt----tgacctagcgggcaactgatgagattcact-tgtgtctcaagcctaaccag----tggttcgtttactttcag
 || || |||||||| || ||||| |||||||| || || |||||||||||||| || || |||||||| || || |||||||| |||||||| || ||||||| | |    | |  ||         |  ||   |||  | | ||  |||     ||  |     |||||   ||  || |||
TGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTTCAATGTCCAGCATTACTTCAAAGgtatcaatattgtaaattactttttttgttgtgtatttccttgtatgcttcagttacaagaaaaacatggttttgtttgttgcag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA10G02410.1 (Glycine max), 5'ss of exon 18
CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg---acctagcgggcaactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcag----------
 || ||||||||||| || ||||| |||||||| || || |||||||||||||| || || ||||| || || || |||||||| ||||||||||| ||||||||| |||   |  ||    |         |  ||   ||   | |||  | |||      |      || | |             
TGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTTCAATGTCCAGCATTACGTCCAAGgtattagttgcaaatttaaacagttttgctctactttgtatttcctttcattcataagtgacaggatagatattgtttttttgttgcag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 5'ss of exon 21
CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttgacctagcgggcaactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcag----------
 ||||||||||| ||||| || || ||||| || ||||||||||||||||| || || || |||||||||||||| |||||||| |||||||| |||||||||   | | |   || |      |       |   |||   | | | |  |    | | |  | |||||  | |           
TGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCTCAATGTCCAGCATTACTTCGAAGgtaac-tctcataaagtgatatgatttccttttatgctttcttttaatgattg--tacttgaccatttacactaaatgctttgcag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 5'ss of exon 21
CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttgacctagcgggcaactgatgagattcacttgtg----tctcaagcctaaccagtggttcgtttact--ttcag
 ||||||||||| ||||| || || |||||||| |||||||| ||||  ||||| | ||| || |||||||| || |||||||| ||||| || || ||||||       ||     |   |  |     |||| ||    |      |     | |||  ||| |    ||| |  | |||
TGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCTCAATGTCAAGCATCACATCTAAGgtaactgaatactctatgaaaagttctaccgatttacacacgggatctttttttcaaacttgtgttcttcttaatactgcag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv17s0000g01550.t01 (Vitis vinifera), 5'ss of exon 22
CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttgacctagcgggcaactgatgagattcacttgtgtctcaagcctaaccagtggttcgtttactttcag--------------------------
 || || ||||| || || || || |||||||| || || || || |||||||| ||||| || ||||||||||| |||||||| ||||| || || |||||  |  ||||  ||    ||  ||  |     || ||||      |           |  ||  |||  | ||||                          
TGGCCCCCCTGGAACAGGCAAGACAATGCTTGCTAAGGCTGTTGCTACTGAAGCTGGTGCAAACTTCATCAATATTTCAATGTCAAGCATCACATCTAAGgttatcattga--taagtagcttcttttttctatcccttgatctctatagtgggttgttatttttttttttctcagctggtttctcatctttcttgttgcag

upper sequence: GRMZM2G052403_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 5'ss of exon 21
CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtat-tatttg-acctagcgggcaactgatgagat-tcacttgtgtctcaagcctaaccagtggttcgtttactttcag---------
 || |||||||| ||||| ||||| |||||||| || || || |||||||| |||||||| ||||| ||||| ||||||||||| || || || || ||||||  ||| || | | |   ||  |||    || | ||  |||    ||  |  |    | |  ||    | ||   |          
TGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATATCAATGTCTAGTATCACTTCAAAGgtaaatatgtgcatcaaaatggtgactatgcagctctcttttgcaagtcttgttttgaaaatatttgacatcctgatattgcttgcag

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|22490580|gb|BU050503.1|BU050503
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|67025653|gb|CO454402.1|CO454402
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|87153787|gb|DY398576.1|DY398576
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|67034427|gb|CO462977.1|CO462977
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGGGTTGGT-AANGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAA
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGT-TTGGTGAA-GGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAA
EST: gi|22490811|gb|BU050734.1|BU050734
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|87152067|gb|DY396856.1|DY396856
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|19058833|gb|BM737500.1|BM737500
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|19058784|gb|BM737451.1|BM737451
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
EST: gi|211048836|gb|FL187596.1|FL187596
EST:     AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACATCGAAG                         TGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT
genomic: AAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGT

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: 130

CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 186

CGGACCTCCTGGCACTGGGAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGTGCTAATTTCATCAATATATCAATGTCGAGCATTACGTCGAAGgtattatttg ... ttactttcagTGGTTTGGTGAAGGGGAGAAGTATGTAAAGGCTGTTTTCTCACTAGCAAGTAAAATAGCCCCCAGTGTTATATTTATCGATGAG