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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgctttatcttttcttgttagccttgtgctactgtagtttatggtgtttgtttttggcttcag

Basic information

species Zea mays
transcript GRMZM2G138195_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 5'ss of exon 26
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgctttatcttttcttgttagccttgtgctactgtagtttatggtgtttgttttt---ggcttcag
 ||||||| ||||| || ||||| || ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||||| ||||||||||||||| ||  ||||     | || | || || |||||     |||| |  |||| || ||  ||| |   |  || ||
GCAGATATAGGTCTCTCCATGGGCATCCAGGGAACTGAAGTTGCCAAGGAGAGTTCTGATATTATCATCTTGGATGACAATTTTGCATCGGTCGTGAGGgtatgtacactg-----tgttctgttattggccttccatgactgcaacttatagtattcttttctctcgcttttag

upper sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA13G00420.1 (Glycine max), 5'ss of exon 26
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgctttatcttttcttgttagccttgtgctactgtagtttatggtgtttgtttttggcttcag---------------------------------
 | |||||||||||  ||||||| || || || || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| || || |||| |||    || |     | |||| | |        |||  ||  | |  |  ||| ||   |||  || | ||                                   
GCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgt----tagccctcatttcttatttgagagattttgaactgttcttataaatgatgcacgtt--tgacatctactttttgaaggttagtactcatttctggcatta

upper sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA17G06520.1 (Glycine max), 5'ss of exon 28
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgctttatcttttcttgttagccttgtgctactgtagtttatggtgtttgttt-----ttggcttcag--------------------------
 | |||||||||||  ||||||| || || || || ||||||||||| ||||| |||||||| ||||| ||||||||||||||||| || || |||| |||    ||       | |||| | | |      |||  ||  | |  |  ||| ||  |||||      |  |||  |                          
GCCGATATTGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCTAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgt----tagtcctcatttcttatttggaagattttgaactgttcttataaatgatgcatgtttaacatctaccttttgaaggactatttctggcattacttgaa

upper sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA09G06890.1 (Glycine max), 5'ss of exon 25
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgcttt-----atcttttcttgtta-gccttgtgctactgtagtttatggtgtttgtttttggcttcag-----------------------------------------------------------------------------------------
 | ||||| |||||  ||||||| || || || || |||||||| || ||||| |||||||| ||||| ||||||||||||||||| || || |||| |||  ||  ||| ||||     || |||  |||||  |  || ||| | |     |     ||    ||||   |                                                                                              
GCCGATATAGGTCTTGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCTGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgtttgt--actactttgagatatttttatttgttctgttttttgccattagtagtggaaatgcactttttgaacactgattgtacaatgagaggtttatatagaagtgaggtgcatttaatattgaagcacaactgatgatgacaattgtgtttctccatggttgtag

upper sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA13G44990.1 (Glycine max), 5'ss of exon 27
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgctttatcttttcttgttagccttgtgctactgtagtttat-ggtgtttgtttttggcttcag---------------------------
 ||||||||||||| || ||||| || || ||||| |||||||| || || ||||| |||||||| ||||||||||| || ||||| || || || | |||| | |   |  |||||    |   |   |  || |     |||  ||| | ||||| |||  ||||    |                            
GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAGgtaagcttgtta-tttattcacttaagcatgtattatatggttgtctttttttggtgtctgtcattggtacaatttcacatgctcaacttagaagttataa

upper sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G00340.1 (Glycine max), 5'ss of exon 27
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgctttatcttttcttgttagccttgtgctactgtagtttatggtgtttgtttttggcttcag-----------------------------
 ||||||||||||| || ||||| || || ||||| |||||||| || || ||||| |||||||| ||||||||||| || ||||| || || || | |||| | |   ||  || | ||||  |||  | | | || |||   | || |     |    ||  |   | |                              
GCAGATATTGGTCTTTCTATGGGCATCCAAGGAACAGAAGTTGCAAAAGAAAGTTCAGATATTATAATCTTGGATGATAACTTTGCATCAGTAGTAAAGgtaagcttgttgtctt-ttttttggtgtctgtcat-tggtacatgatttcacatgctcaacttaagaacttatatacatttctttggcaatgatttgcctag

upper sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G18180.1 (Glycine max), 5'ss of exon 25
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgcttt-----atcttttcttgtta-gccttgtgctact-gtagtttatggtgtttg-tttttggcttcag-------------------------------------------------------------------------------------------
 | ||||| |||||| ||||||| || || || || |||||||| || ||||| || ||||| ||||| ||||||||||||||||| || || |||| |||  ||  ||| ||||     || ||   |||||  |  || ||  | | ||||     |   |    ||||||  | | |                                                                                           
GCCGATATAGGTCTAGCAATGGGTATCCAAGGTACAGAAGTTGCCAAAGAGAGCTCCGATATCATTATTTTGGATGACAATTTTGCTTCAGTTGTGAAGgttagt--actactttgagatattttaatttgttctgttttttgtcattagtagaagtagaaatgcactttttgaatactgattgtacaatgagaggtttatatagaattgaggtgcattgaatatttgaagcacaactgatgatgacaattgtttttctccatggttgtag

upper sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT5G57110.1 (Arabidopsis thaliana), 5'ss of exon 27
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgt------acgttaactgctttatcttttcttgttagccttgtgctactgtagtttatggtgtttgt---ttttggcttcag----------------------------------------------------------------------------------------------------------------------
 |||||||||||||  | ||||| ||    ||||| ||||| |||||||||||||| || || || |||||||||||||| ||||| || || || | |||      |  || |||  ||| |  ||| | | |    ||||   |     || |          |   |     |||||                                                                                                                       
GCAGATATTGGTCTTGCTATGGGAATAGCAGGAACAGAAGTGGCTAAGGAGAGTTCGGACATCATCATCTTGGATGACAACTTTGCTTCAGTTGTCAAGgtttattcaaattcacttttttctactttatagattcatttgttggataaaggtctgcaagacacataaatccctacttcaatagattttttttgtgaatccatgtatactatgtgtagatccaagaatgcatttttcgtaactgaatttgttgctactaagtattccaaccttaatttgtggtgatatatattatatag

upper sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 5'ss of exon 25
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgcttta-----------------tctttt------cttgttagccttgtgctactgtagtttatggtgtttgtttttggcttcag
 ||||||| ||||| || ||||| ||    |||||||||||||| || ||||||||||| || ||||| ||||||||||||||||| || || || | |||  ||  ||| | | |                 |||| |          | | | || ||||  | || |  ||    | |||||     | |||
GCAGATATAGGTCTCTCTATGGGTATATCAGGAACTGAAGTTGCAAAAGAGAGTTCTGACATCATTATTTTGGATGACAATTTTGCTTCAGTAGTAAAGgttagtctactacatcaaatatagaaacatgtgatcttctacattatccttcatctttatgcttttctaatcaataaactctgtttactcttccag

upper sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 27
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgt-taactgctttatcttttcttgtta---gccttgtgctactgtagtttatggtgtttgtttttggcttcag-----------------------
 ||||||| ||||| || ||||| ||||| |||||||||||||| || || || || || || |||||||||||||| || |||||||| || || | |||  || |||       || | |    || |   | |||| |    |||||||     | |   || ||   || |                        
GCAGATATAGGTCTCTCTATGGGCATTCAAGGAACTGAAGTTGCAAAAGAAAGCTCAGACATCATTATCTTGGATGATAACTTTGCCTCAGTTGTAAAGgttagtgtaagcaaaccatttatgtgagtaaattgtcttgggaatttgtagttatgattctaccttgttatatttaaaacaaaaatactgtcaatccttt

upper sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 5'ss of exon 28
ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaactgctttatcttttcttgttagccttgtgctactgtagtttatggtgtttgtttttggcttcag----------------------------
 |||||||||||||  ||||||| |||   ||||| || ||||| || ||||| ||||| || ||||||||||||||||||||||| || || || | |||  ||    ||| || |       | |||         ||    |  |     ||  ||    |  |   |                             
GCAGATATTGGTCTTGCAATGGGCATTTCAGGAACAGAGGTTGCAAAAGAGAGCTCTGACATCATTATCTTGGATGACAATTTTGCGTCAGTTGTCAAGgttagtctg-tgcattgtaagagtattttaagtgatcaatagcaaatatgtaaatgactgcaactcccacaaatgaatgttttcatccaatcttgaacaaa

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: 90

ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaac ... ttggcttcagGTTGTCAGGTGGGGCCGATTGGTATATGCAAACATACAAAAGTTTATACAGTTCCAACTAACAGTCAATGTCGCAGCTCTGATAATCAATGTAGTTGCTG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 34

ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaac ... ttggcttcagGTTGTCAGGTGGGGCCGATTGGTATATGCAAACATACAAAAGTTTATACAGTTCCAACTAACAGTCAATGTCGCAGCTCTGATAATCAATGTAGTTGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 36

ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaac ... ttggcttcagGTTGTCAGGTGGGGCCGATTGGTATATGCAAACATACAAAAGTTTATACAGTTCCAACTAACAGTCAATGTCGCAGCTCTGATAATCAATGTAGTTGCTG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 208

ACAGATATTGGTCTATCAATGGGGATTCAGGGAACTGAAGTTGCTAAGGAGAGTTCTGATATTATTATCTTGGATGACAATTTTGCCTCGGTCGTGAGGgtacgttaac ... ttggcttcagGTTGTCAGGTGGGGCCGATTGGTATATGCAAACATACAAAAGTTTATACAGTTCCAACTAACAGTCAATGTCGCAGCTCTGATAATCAATGTAGTTGCTG