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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTTCGTAAATTAAGAAATTTTAGGACTTTCTCTCCCTATGATTTGGACACGCCAACCAATACTGgtaagtaacttggccatgaacagttagaaaggtgcacatgcttgcatttgcatatgtataattatagctatcgggagagggtcattcgatgtatgaaatg...

Basic information

species Zea mays
transcript GRMZM2G324540_T02
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G324540_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os10g32880.1 (Oryza sativa), 5'ss of exon 13
ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTTCGTAAATTAAGAAATTTTAGGACTTTCTCTCCCTATGATTTGGACACGCCAACCAATACTGgtaagtaacttggc-catg---aacagtt--agaaaggtgcacatgct-----tgcatttgcatatgtataattatagctatcgggagagggtcattcgatgtatgaaatg
||||||||||  ||||| || ||||||||||||||||| ||||||||||| ||||||||  | || || ||||| |  ||||||||||| ||| |||||||| ||||| || ||||    ||| |   || ||  ||   ||| |     ||| |     | ||||||  |||||| | |  | |||  |   | ||           
ACTGCTGCTCTCGATGGAGTCAAGCTTTGGGATCTTCGAAAATTAAGAAACTTTAGGACGATATCACCTTATGACTCAGACACGCCAACAAATTCTGgtaaggaactttgcgcatgctccacactcacagtaaattgtgaatggtgcatgtgcttcgatgtgtgtatagatatagccaacaagcgagattatgttga-----------

upper sequence: GRMZM2G324540_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA10G26870.1 (Glycine max), 5'ss of exon 15
ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTTCGTAAATTAAGAAATTTTAGGACTTTCTCTCCCTATGATTTGGACACGCCAACCAATACTGgtaagtaacttggcc-atgaacagttagaaaggtgcacatgcttgcatttgcatatgtataattatagctatcgggagagggtcattcgatgtatgaaatg--
||||||||||||||||||||||||||||||||||| |||||||| |  || || |||| |||  |||| |||||||  || || || || |   | ||||   |  ||  |   |  |  |  | | |    |  ||   |  | |  |   |    | || ||  ||     |  || | | |   | | |        
ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTACGTAAATTGAAGAACTTCAGGAATTTTGCTCCATATGATTCAGAAACACCGACGAGCTCCGgtattcattttcacttgttgatggccatataa---cctatttatataataccggttaggaagttgtacatacttcaaagggtttactatctttttagtcctta

upper sequence: GRMZM2G324540_T01 (Zea mays), 5'ss of exon 15
lower sequence: GLYMA20G21330.1 (Glycine max), 5'ss of exon 15
ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTTCGTAAATTAAGAAATTTTAGGACTTTCTCTCCCTATGATTTGGACACGCCAACCAATACTGgtaagtaacttggccatgaacagttagaaaggtgcacatgcttgcatttgcatatgtataa-ttatagctatcgggagaggg--tcattcga----tgtatgaaatg---
||||||||||||||||||||||||||||||||||| |||||| | |  || || |||| |||  |||| ||||||| ||| || ||||| |   | ||||   |  ||  |  |  |  |  | | |    |  ||  ||  || | |   |  | || || ||  |||    | |||   ||||   |    ||| ||   ||   
ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTACGTAAACTGAAGAACTTCAGGAATTTTGCTCCATATGATTCGGAAACACCAACGAGCTCCGgtattcattttcac--ttgatggcaatataa---cctatatttatatatactggttaagaagttgtacatatttcaaaaggccttcatcttaattctgtgtgtcttgcag

upper sequence: GRMZM2G324540_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv05s0049g01840.t01 (Vitis vinifera), 5'ss of exon 15
ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTTCGTAAATTAAGAAATTTTAGGACTTTCTCTCCCTATGATTTGGACACGCCAACCAATACTGgtaagtaacttggccatgaacag----ttagaaaggtgcacatgcttgcatttgcatatgtataattatagctatcgggagagggtcattcgatgtatgaaatg
||||| |||||||||||||||||||| |||||||| || ||||| || |||||  |||| ||  | || |||||||   | ||  |||| ||  |||||| |||    |   ||  || |    ||  ||   | |  |    |  |  || ||   || | || |   ||  |||  |  ||        ||  ||||| 
ACTGCAGCTCATGATGGTGTTAAGCTGTGGGATCTACGAAAATTGAGGAATTTCCGGACCTTTACACCATATGATTCAAATACAGCAACAAACTCTGgtatgtattcagtttattcaccgagtttttaaaccttacgaagagattaagctgtat---taaacttctgattaagggggaaaagtttaaactagttggaaat-

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|32835508|gb|CD975186.1|CD975186
EST:     AAATTTTAGGACTTTCTCTCCCTATGATTTGGACACGCCAACCAATACTG                         TGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA
genomic: AAATTTTAGGACTTTCTCTCCCTATGATTTGGACACGCCAACCAATACTGgtaagtaact ... ttccttgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAA




















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: 48 (upstream exon), 49 (downstream exon)
Score: 273

ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTTCGTAAATTAAGAAATTTTAGGACTTTCTCTCCCTATGATTTGGACACGCCAACCAATACTGgtaagtaact ... ttccttgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 105

ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTTCGTAAATTAAGAAATTTTAGGACTTTCTCTCCCTATGATTTGGACACGCCAACCAATACTGgtaagtaact ... ttccttgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTTCGTAAATTAAGAAATTTTAGGACTTTCTCTCCCTATGATTTGGACACGCCAACCAATACTGgtaagtaact ... ttccttgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 99

ACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTTCGTAAATTAAGAAATTTTAGGACTTTCTCTCCCTATGATTTGGACACGCCAACCAATACTGgtaagtaact ... ttccttgcagTGGAATTTGATTTTAGTGGAAACTATCTTGCCATTGGTGGTTCAGATATAAG