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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactcacgatcaatatgtattggtagtgttttttagtgtatgtgtatcatcacaacataagtctataactgtgatttcattcttgtag

Basic information

species Zea mays
transcript GRMZM2G145107_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G145107_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g58080.1 (Oryza sativa), 5'ss of exon 10
ACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactcacgatcaatatgt--------attggtagtgttttttagtgtatgtgtatcatcacaacataa--gtctataactgtgatttcattcttgtag
||| || |||||||||||||| |||||||| | |||||||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| | ||||||| ||| ||| ||||| | | ||| | | | ||| | || | | || | | | | ||| || |
ACGTGAGGTTTACCATGGGGACCCAAATGGCAACTTGAGTGAAAGGAAAGCTTATGACAACGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaacccttgatcaatgtgtttactataatttgtagtatgtcgctatgtttagatgctgttacaccccaatcatttctagcctttctgt-atttttat--

upper sequence: GRMZM2G145107_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA08G40980.1 (Glycine max), 5'ss of exon 10
ACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactcacgatcaa---tatgtattggtagtgttttttagtgtatgtgtatc--atcacaacat--aagtctataactgtgatttcattcttgtag--------------------------------------------------------------------
| |||||||| ||||| |||||||| || || ||| | |||||| | || || ||||||||||||||||||||||||||||||| ||||||||||| ||| | ||| |||| || | || | | | | || | | | || | | | | | | ||| ||| |
GAGAGAAGTTTATCATGGTGATCCAAAAGGGGACACTTCTGAAGTAGATCTTTATGATCAAGGAGTTAGAGAAGGTGCATTTGGTTTGCTATTGAATTCTgtaagaactcaagattgagcatatttatttttaaagaaacttgtcacaagctttactgatgatgatctggaacttttttatttttcttttattaaactgactttctggatttttatcctgcccaattattgatctgagtcatctgacattgcttttatggcttgttag

upper sequence: GRMZM2G145107_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA18G15950.1 (Glycine max), 5'ss of exon 11
ACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactcacgatcaatatgtattggtagtgttttttagtgtatgtgtatcatca-caacataagtctataactgtgatttcattcttgtag----------------------------------------------------------------------------
| |||||||| ||||| |||||||| || | ||| | |||||| | || || ||||||||||||||||||||||||||||||| ||||||||||| || | |||| | | | | | | | | | | | ||| |||| | | | ||||| ||
CAGAGAAGTTTATCATGGTGATCCAAAAGGGGGCACTTCTGAAGTAGATCTTTATGATCAAGGAGTTAGAGAAGGTGCATTTGGTTTGCTATTGAATTCTgtaagaactcaaaattga-gcatatttattttctcaagagatttgtcacaagctttagtgatgatgatctggaacttttttatttttcttttattaaattgactttctggatttttatcctgcccaattattgatctgagtcatctgacattgcttttatggcttgatag

upper sequence: GRMZM2G145107_T01 (Zea mays), 5'ss of exon 10
lower sequence: Vv01s0026g01960.t01 (Vitis vinifera), 5'ss of exon 10
ACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactcacgatcaatatgtattggtagtgttttt---tagtgtatgtgtatcatcacaacataagtctataactgtg-atttcattcttgtag---------------------------------------------------------------------------
| |||||||| ||||||||||| || || ||| | || ||||| ||||| |||||| ||||||||||||||||||||||||||||||||||||||||||| || | | | | ||||| || ||| | | || | | || |||| | || | || | | |
TAGAGAAGTTTATCATGGGGATCCTAAAGGGGATGAGTCTGCAGTTAAAGCATATGATGCTGGTGTTAGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactcaaaattgagcatcagcaattctatttttagatactgttcatagttaattgaatctaaaaataataaatttgtaaaatatattaatggcaaggaattcatcaagttctattcattttacattgccaataatagttaattcaaaagtatatttttgttgcatag

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|28361756|gb|CB240112.1|CB240112
EST:     CTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCA                         GTTGTCCTTGGCGTTGGTTCATTCCTTGTTGATCCACTATGCCGGATGATT
genomic: CTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactc ... attcttgtagGTTGTCCTTGGCGTTGGTTCATTCCTTGTTGATCCACTATGCCGGATGATT
EST: gi|89756976|gb|DY686775.1|DY686775
EST:     CTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCA                         GTTGTCCT-GGCCGT-GGTTCATTCCTTGTTG-TCCACTATG
genomic: CTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactc ... attcttgtagGTTGTCCTTGGC-GTTGGTTCATTCCTTGTTGATCCACTATG
EST: gi|29544547|gb|CB604927.1|CB604927
EST:     CTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCA                         GTTGTCCTTGGCGTTGGTTCATTCCTTGTTGATCCACTATGCCGGATGATT
genomic: CTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactc ... attcttgtagGTTGTCCTTGGCGTTGGTTCATTCCTTGTTGATCCACTATGCCGGATGATT
EST: gi|28361547|gb|CB239903.1|CB239903
EST:     CTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCA                         GTTGTCCTTGGCGTTGGTTCATTCCTTGTTGATCCACTATGCCGGATGATT
genomic: CTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactc ... attcttgtagGTTGTCCTTGGCGTTGGTTCATTCCTTGTTGATCCACTATGCCGGATGATT
EST: gi|211187551|gb|FL182401.1|FL182401
EST:     TGGTTTGCTATTGAATTCA                         GTTGTCCTTGGCGTTGGTTCATTCCTCGTTGATCCACTATGCCGGATGATT
genomic: TGGTTTGCTATTGAATTCAgtaagaactc ... attcttgtagGTTGTCCTTGGCGTTGGTTCATTCCTTGTTGATCCACTATGCCGGATGATT

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: 83

ACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactc ... attcttgtagGTTGTCCTTGGCGTTGGTTCATTCCTTGTTGATCCACTATGCCGGATGATTGGTGCAAGATTAGTTTGGGCCATTAGCAACTTCACGGTGTTTATTTGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

ACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactc ... attcttgtagGTTGTCCTTGGCGTTGGTTCATTCCTTGTTGATCCACTATGCCGGATGATTGGTGCAAGATTAGTTTGGGCCATTAGCAACTTCACGGTGTTTATTTGCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 205

ACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactc ... attcttgtagGTTGTCCTTGGCGTTGGTTCATTCCTTGTTGATCCACTATGCCGGATGATTGGTGCAAGATTAGTTTGGGCCATTAGCAACTTCACGGTGTTTATTTGCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 126

ACGCGAAGTTTACCATGGGGATCCAAATGGAGATTTGAGTGAGAGGAAAGCTTATGACAATGGTGTCCGAGAAGGTGCATTTGGTTTGCTATTGAATTCAgtaagaactc ... attcttgtagGTTGTCCTTGGCGTTGGTTCATTCCTTGTTGATCCACTATGCCGGATGATTGGTGCAAGATTAGTTTGGGCCATTAGCAACTTCACGGTGTTTATTTGCA