Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACACATCCATCAGAGTTTTTCTTGGGGTGGTTCTGAAATAAAAGTGTGGCGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatcagtatattatttacagatataaaagccttagcatcactatttcactaagctcgaagtcctaaaaccttgtactgttttgtaagtggcaata...

Basic information

species Zea mays
transcript GRMZM2G141399_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141399_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os08g09230.2 (Oryza sativa), 5'ss of exon 8
TACACATCCATCAGAGTTTTTCTTGGGGTGGTTCTGAAATAAAAGTGTGGCGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatcagtatattatttacagatataaaagccttag--catcact---atttcactaagctcgaagtcctaaaaccttgtactgttttgtaagtggcaata
| ||  | | ||| || ||||||| ||||||| | ||||| |||||||||  ||||||||| |||| ||| | |||||||||| |||||||||||||||||||||   ||    ||| || ||| | | | |    ||||   || |||    |||||| ||   |    |||  || |||| ||||   |  |     |     
TGCATGTACGTCAAAGCTTTTCTTTGGGTGGTACAGAAATTAAAGTGTGGTTTGGACTAGTTGAAGACCTGTCTGTTTACTTCTTGGAACCTCAAAATGGgtatgttgcatctcattcttcacacaaacatagctattagtctattactcttgtttcacgaaaaccatcatccctaatccttatactagctaatgcacag-----

upper sequence: GRMZM2G141399_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G27480.1 (Glycine max), 5'ss of exon 9
TACACATCCATCAGAGTTTTTCTTGGGGTGGTTCTGAAATAAAAGTGTGGCGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatcagtatattatttacagatataaaagccttagca--tcactatttcactaagctcgaag-tcctaaaaccttgtactgttttgtaagtggcaata
|  ||   ||  | || | ||| ||||| ||  ||||||||||||| |||| ||||  ||| |||||||| | ||| |||||  |||| ||||||||||||||         ||  |    || | | |  ||   ||  ||  | | | ||||  || ||  ||   || | | |  ||| |    |   |   |   |   
TTGACTATCACAAAAGCTATTCCTGGGGAGGCACTGAAATAAAAGTATGGCATGGAAAAGTTGAAGGCCTCTCTGTCTACTTTTTGGAGCCTCAAAATGGgtaaatgctttgattctccacactgttctctaatttttgtcaattaagtgtttc-ttatgcctgagcctctttatattttggaaaaataactttttcatat--

upper sequence: GRMZM2G141399_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA15G11500.1 (Glycine max), 5'ss of exon 9
TACACATCCATCAGAGTTTTTCTTGGGGTGGTTCTGAAATAAAAGTGTGGCGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatcagtatattatttacagatataaaagccttagcatcactatttcactaagctcgaagtcctaaaaccttgtactgttttgtaagtggcaata
|  ||   ||  | || | ||| ||||| ||  ||||||||||||| |||| ||||  ||| |||||||| | ||| |||||  |||| ||||||||||||||   |     ||  |    || | | |  ||   ||  |       | |  || |  ||  || |       |   |    | | |    |  |||| 
TTGACTATCACAAAAGCTATTCCTGGGGAGGGACTGAAATAAAAGTATGGCATGGAAAAGTTGAAGGCCTCTCTGTCTACTTTTTGGAGCCTCAAAATGGgtaaatactttgattctccacactgttctctaatgtttgtctattaagtgtttcttatgtctgagcctctttttcacatcaactctggaccctatcaatt

upper sequence: GRMZM2G141399_T02 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA07G39040.1 (Glycine max), 5'ss of exon 6
TACACATCCATCAGAGTTTTTCTTGGGGTGGTTCTGAAATAAAAGTGTGGCGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatc-agtatattatttacagatataaaagccttagcatcactatttcactaagctcgaagtcctaaaaccttgtactgttttgtaagtggcaata---
| ||    ||    |  | || |||||||||  ||||||||||||| |||| ||||   || ||||| || | ||| |||||| ||||||||||||||| ||| | ||   |     ||| |  | |  |         | |||| |    | ||| || |  |    |  | |      |  |  |  ||| | |  ||    
TTCAATATCACAGAAACTATTTTTGGGGTGGGACTGAAATAAAAGTATGGCATGGAAAGGTGGAAGGTCTCTCTGTCTACTTCTTGGAACCTCAAAATGCgtaagaatttggcgctctatctttaaaagttgttagga-aacatcccctcataactcaggtttactctcacagaa---agaaagcctaataaatagagatgagt

upper sequence: GRMZM2G141399_T02 (Zea mays), 5'ss of exon 8
lower sequence: AT1G11720.1 (Arabidopsis thaliana), 5'ss of exon 7
TACACATCCATCAGAGTTTTTCTTGGGGTGGTTCTGAAATAAAAGTGTGGCGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatca-gtatattatttac--agatataaaagccttagcatcactatttcactaag-ctcgaagtcctaaaaccttgtactgttttgtaagtggcaata
| ||  |  |    || | |   ||||| ||  ||||||||||||| |||| ||||  ||| ||||||||||  ||||||||| | || || ||||||||||  || | | | |||||  |     || | |     | ||    |||  || ||   | | |  ||||    ||    ||||  |   |||   || |||   
TGCAATTTAACAGAAGCTATCACTGGGGAGGAACTGAAATAAAAGTTTGGCATGGAAAAGTAGAAGGCCTTTCGGTTTACTTCTTAGATCCACAAAATGGgttagctttatgcatattgctctttaagctctttccacatttcattcatcatctcttgagggcatgaag----aagttgttgtcgttgcttgactgttgcag--

upper sequence: GRMZM2G141399_T02 (Zea mays), 5'ss of exon 8
lower sequence: Vv10s0116g01730.t01 (Vitis vinifera), 5'ss of exon 11
TACACATCCATCAGAGTTTTTCTTGGGGTGGTTCTGAAATAAAAGTGTGGCGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatcagtatattatttacagatataaaagccttagcatcactatttcactaagctcgaagtcctaaaaccttgtactgttttgtaagtggcaata----
| ||     |     | | ||  ||||||||  ||||||||||||| |||  ||||  ||| |||||||||| |||||||||  | || ||||||||||||||  |  |||||  |   |||||  | | | |  | |  ||| | |||||   || |         || |    |  |  |  |   ||  |  || |     
TTCAGTATAAGAGATGCTATTTCTGGGGTGGAACTGAAATAAAAGTTTGGTTTGGAAAAGTGGAAGGCCTTTCTGTTTACTTTTTAGAGCCTCAAAATGGgtaatc--cagtagttctgttacaccttttaga--catgccattattattttggtaggaatttgtatctcatttttactgttcatgcatatatttcagttaact

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|33091960|gb|CF051954.1|CF051954
EST:     CGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGG                         GATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGG
genomic: CGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatca ... ttttttttagGATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGG
EST: gi|31361027|gb|CD445384.1|CD445384
EST:     CGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGG                         GATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGG
genomic: CGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatca ... ttttttttagGATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGG
EST: gi|31357767|gb|CD442124.1|CD442124
EST:     CGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGG                         GATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGG
genomic: CGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatca ... ttttttttagGATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGG
EST: gi|67022688|gb|CO451437.1|CO451437
EST:     CGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGG                         GATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGG
genomic: CGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatca ... ttttttttagGATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGG
EST: gi|32933471|gb|CF038283.1|CF038283
EST:     CGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGG                         GATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGG
genomic: CGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatca ... ttttttttagGATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGG

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: 109

TACACATCCATCAGAGTTTTTCTTGGGGTGGTTCTGAAATAAAAGTGTGGCGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatca ... ttttttttagGATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGGCTTCTTCTGTCGTTCTGCTCTAGAGTTTCTCCTCCAAAGTGGATCTTCT


Block sizes: 49 (upstream exon), 17 (downstream exon)
Score: 13

TACACATCCATCAGAGTTTTTCTTGGGGTGGTTCTGAAATAAAAGTGTGGCGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatca ... ttttttttagGATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGGCTTCTTCTGTCGTTCTGCTCTAGAGTTTCTCCTCCAAAGTGGATCTTCT


Block sizes: 46 (upstream exon), 30 (downstream exon)
Score: 7

TACACATCCATCAGAGTTTTTCTTGGGGTGGTTCTGAAATAAAAGTGTGGCGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatca ... ttttttttagGATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGGCTTCTTCTGTCGTTCTGCTCTAGAGTTTCTCCTCCAAAGTGGATCTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

TACACATCCATCAGAGTTTTTCTTGGGGTGGTTCTGAAATAAAAGTGTGGCGTGGACTAGTCGAAGGCCTTTGTGTTTACTTCCTGGAACCTCAAAATGGgtatgcatca ... ttttttttagGATGTTTGGAGTCGGATATGTATATGGCAGGGACGATGACCGCCGATTTGGCTTCTTCTGTCGTTCTGCTCTAGAGTTTCTCCTCCAAAGTGGATCTTCT