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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATATTTCTGCATCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgtattcactgtttccacttattgaccaactcttgtgttttaagttaaccagcactaatgcagtttcgtccatgagctggtcaccattgttgtctactctg...

Basic information

species Zea mays
transcript GRMZM2G116840_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116840_T06 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 5'ss of exon 4
GTTATATTTCTGCATCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgtat--tcactgtttccacttattgaccaactcttgtgttttaagttaaccagcactaatgcagtttcgtccatgagctggtcaccattgttgtctactctg
|| |||||||| |||||||| || |||||||| ||||||||||||||||| || |||||||||||||   | | ||| | | | ||||||   |    |   | ||   ||         |  |   |     ||||| |  |  ||     |||     | | | 
GTCATATTTCTTCATCCAGCGCCAATGCATCCGCACATTTACAGCAATGGGCATATCTGTTTAGgtaaaatgattgtatgctcctattgatgcataaataattgttgttttcgttcttgatgcttttgcccactccattaattc-tcttgggtgtacagcatttt-

upper sequence: GRMZM2G116840_T06 (Zea mays), 5'ss of exon 2
lower sequence: AT1G75440.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTATATTTCTGCATCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgtat-tcactgtttccact--tattgaccaactcttgtgttttaagttaaccagcactaatgcagtttcgtccatgagctggtcaccat-tgttgtctactctg
|| || ||||| |||||||| ||  ||||||| ||||||||||||||||| || || ||| ||||||| ||||||| ||| ||  | |     | ||  |   | ||  |||    |  |   || || |||| |  |   ||||||||   | ||| |||       
GTGATTTTTCTTCATCCAGCTCCTCTGCATCCTCACATTTACAGCAATGGGCATATTTGTCTAGgtatgtcactgtgtcctctgttttctgataccttcttactcttttgttggttattatctat-cactttc-tttacttgctggtcatactatgtggtccgaat--

upper sequence: GRMZM2G116840_T06 (Zea mays), 5'ss of exon 2
lower sequence: AT5G42990.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTATATTTCTGCATCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgtattcactgtttccacttattgaccaactcttgtgttttaagttaaccagcactaatgcagtttcgtccatgagctggtcaccattgttgtctactctg-----
|| || ||| | |  ||||||||| | ||||| || ||||||||||||||||| || ||||||||||   | | |   || |  ||   ||   |||    |||   ||  |    |||  |   |||||    |   ||| |   | | |  ||| |           
GTGATTTTTGTTCCACCAGCACCGTTACATCCTCATATTTACAGCAATGGACATATTTGTTTAGgta---attttactcattgtttctacactacttactctttgcatttgctcttactt-tttggtttctctgaaatgctagct-caagtcatgtgtgtgtcaatcaa

upper sequence: GRMZM2G116840_T06 (Zea mays), 5'ss of exon 2
lower sequence: AT1G45050.1 (Arabidopsis thaliana), 5'ss of exon 4
GTTATATTTCTGCATCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgtattcactgtttccacttattgaccaactcttgtgttttaagttaaccagcactaatgcagtttcgtccatgagctggtcaccattgttgtctac-tctg----
||  | ||| |   ||| |||||    |||||||| || |||||||||||||| || ||||||||||||   || |  | |||  | ||   ||  | ||  |    |||        || |   | |     || | | | |||   |||| | | ||  | |     
GTAGTGTTTGTTTCTCCGGCACCTTCACATCCACATATATACAGCAATGGACATATTTGTTTAGgtattgcttgctatctcttggttactgtctgctctgcatatgcttatgt----ttagttttgatcaaagcaagggtttgtcga-attgatatgtagatgtagaat

upper sequence: GRMZM2G116840_T06 (Zea mays), 5'ss of exon 2
lower sequence: Vv18s0001g13180.t01 (Vitis vinifera), 5'ss of exon 4
GTTATATTTCTGCATCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgta-ttcactgtttccacttattgaccaactcttgtgttttaagttaacca-gcactaatgcagtttcgtccatgagctggtcaccattgttgtctactctg
||| | ||| | |  ||||| ||  ||||||| ||||| ||||||||||| || ||||||||||||| |||  |  |||||     ||   |    || |||||    ||   || | | | |||    |   |  || |  |  | |  ||| |     | ||||
GTTGTTTTTGTCCCGCCAGCTCCTCTGCATCCTCACATATACAGCAATGGGCATATCTGTTTAGgtaattccataattccagcacatgtttatagattttgtttctgattggacatgaattcatgt--ctgttttaattatttcatgatgattttatgtgattctg

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|211201084|gb|FL470739.1|FL470739
EST:     TCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAG                         ATTGGTCCACTGGCTATGCCAAGAAATTCCTAGAAATATTACTAACTAACC
genomic: TCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgtattcactg ... ttttttccagATTGGTCCACTGGCTATGCCAAGAAATTCCTAGAAATATTACTAACTAACC
EST: gi|211372658|gb|FL212545.1|FL212545
EST:     TCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAG                         ATTGGTCCACTGGCTATGCCAAGAAATTCCTAGAAATATTACTAACTAACC
genomic: TCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgtattcactg ... ttttttccagATTGGTCCACTGGCTATGCCAAGAAATTCCTAGAAATATTACTAACTAACC
EST: gi|89248057|gb|DY619843.1|DY619843
EST:     TCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAG                         ATTGGTCCACTGGCTATGCCAAGAAATTCCTAGAAATATTACTAACTAACC
genomic: TCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgtattcactg ... ttttttccagATTGGTCCACTGGCTATGCCAAGAAATTCCTAGAAATATTACTAACTAACC

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: 27 (upstream exon), 44 (downstream exon)
Score: 7

GTTATATTTCTGCATCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgtattcactg ... ttttttccagATTGGTCCACTGGCTATGCCAAGAAATTCCTAGAAATATTACTAACTAACCATGATTCCATGAGATGGCAACTATCACTGGCCCCTTAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 10

GTTATATTTCTGCATCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgtattcactg ... ttttttccagATTGGTCCACTGGCTATGCCAAGAAATTCCTAGAAATATTACTAACTAACCATGATTCCATGAGATGGCAACTATCACTGGCCCCTTAAG


Block sizes: 46 (upstream exon), 41 (downstream exon)
Score: 8

GTTATATTTCTGCATCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgtattcactg ... ttttttccagATTGGTCCACTGGCTATGCCAAGAAATTCCTAGAAATATTACTAACTAACCATGATTCCATGAGATGGCAACTATCACTGGCCCCTTAAG


Block sizes: 20 (upstream exon), 30 (downstream exon)
Score: 2

GTTATATTTCTGCATCCAGCACCGATGCATCCACACATTTACAGCAATGGACACATCTGTTTAGgtattcactg ... ttttttccagATTGGTCCACTGGCTATGCCAAGAAATTCCTAGAAATATTACTAACTAACCATGATTCCATGAGATGGCAACTATCACTGGCCCCTTAAG