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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttgaattgatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaacatatttgtgcag

Basic information

species Zea mays
transcript GRMZM5G821611_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g42370.3 (Oryza sativa), 5'ss of exon 3
GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttgaattgatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaa-catatttg-tgcag
||| ||||| ||||||||||||||||||||||| || ||||| |||||||||||||||||||||||||||||||||||||| ||||| ||||||||||| ||||||  |  |   | | ||| ||| |       ||||||   ||| | |  |    |||||  ||             ||||||||| || |||| | | |    ||||||||      || | |       |||   ||    || ||||| ||||| || |||||||| |||||
GCTTTACCGGCCACCTCGATGCTCACACTGTTCGATATGCAACAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTTGGCCAATGCATAGGACTTgtaagtatcatgtttttccagcagttctgtacctatccttaccgtaggaaagaca---tgtgcgtatt------------tgtttggagttattcttccagtgc---ttttcatt-----gagctct-------cttcaaatcaacttgagcctaatcataaagcatatttggtgcag

upper sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G05670.2 (Glycine max), 5'ss of exon 3
GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttgaattgatgtttggaggtactctttctgggtagattttcattttt-ttaagttgttgactaactttctattctgttaagcctgatcatcaacatatttgtgcag
||| ||| | || ||||||||||| ||||| || || || ||||||||||||||||||||||| ||||||||||| ||||| || ||||| || || |||||| |||      |||  |   ||| |    || ||  || ||||       ||    ||||   | |           |||||| | || |        | |||| ||  |    || ||||||                                                    
GCTCTACAGGCCTCCTCGATGCTCGCACTGCTCAATCTGTAATAACTGTGTGGAACGGTTTGACCATCACTGTCCTTGGGTTGGGCAGTGTATTGGGCTGgtatgttg-----gatctt--ttgtctcttgagtgttattttattctttttttctttttgtgtgaaga-----------atgttttgggggaa-------gagtagcttaaccccattgttaagt----------------------------------------------------

upper sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA19G27160.1 (Glycine max), 5'ss of exon 3
GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttgaattgatgtttggaggtactctttctgg-gtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaacatatttgtgcag
||| ||| | || ||||||||||| ||||| || || || ||||||||||||||||||||||||||||||||||| ||||| || ||||| || || ||||||||||      |||  ||  | |   |  || ||  || ||||       ||    ||||   ||      |||  |    ||      | |   | ||    |||                                                                     
GCTCTACAGGCCTCCTCGATGCTCGCACTGCTCAATCTGTAATAACTGTGTGGAACGGTTTGATCATCACTGTCCTTGGGTTGGGCAGTGTATTGGGCTGgtaagttg-----gatcttatatctccca--agtgttattttattcttttt-tctttttgtgtgaatttgggggaagagtatcttaatcccattaagtgtgacagaga---------------------------------------------------------------------

upper sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G26140.2 (Glycine max), 5'ss of exon 3
GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgct------agctg--ttttaatagcgtccttatattagaacaatcgcgg-tgtgcacatacacttgaattgatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaacatatttgtgcag
||| ||| | || |||||||| || ||||| || ||||| |||||||||||||||||||||||||| || ||||| ||||| || |||||||| || |||||||||||  |    || |      |  ||  ||||||| | |||        ||||    | | | |  ||| | | ||| |  ||| | | ||| |  |                                                                                    
GCTCTACAGGCCTCCTCGATGTTCTCACTGCTCAATTTGTAATAACTGTGTGGAACGGTTTGATCACCATTGTCCCTGGGTTGGGCAGTGCATTGGGCTGgtaagttagaccttttgtttgacaaaattgatttttaattgagtctgatctgcagaatttcctctgctaggcagaaagact-ggcttggtatctggggtga------------------------------------------------------------------------------------

upper sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA02G07190.1 (Glycine max), 5'ss of exon 3
GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttgaattgatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaacatatttgtgcag
||| ||| | || |||||||| || ||||| || ||||| |||||||||||||||||||||||||| || ||||| ||||| || |||||||| || |||||||||||   ||  |  |   ||    ||| |  |  | ||  |  | |      |  |       |    |     ||      ||   ||  | ||||||                                                                         
GCTCTACAGGCCTCCTCGATGTTCTCACTGCTCAATTTGTAATAACTGTGTGGAACGGTTTGATCACCATTGTCCCTGGGTTGGGCAGTGCATTGGGCTGgtaagtta---gaccttttgtttgacaaaattgatttttaattgtgaatctgctctgcagaatttccaatgctaggcagaaagactga--cacggtatctggggt-----------------------------------------------------------------------

upper sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G08200.1 (Glycine max), 5'ss of exon 2
GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttgaattgatgtttggaggtactctttctgggtagattt-tcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaacatatttgtgcag
||| ||||| || ||||||||||| ||||| || || || ||||||||||||||||||||||| ||||||| ||| ||||| || ||||| || || || ||| |||      |||  |   ||| |   ||| ||  || ||||          |  | | |   |     ||||   |||||| | || |        | |||| ||  ||   || ||||||                                                    
GCTCTACCGGCCTCCTCGATGCTCGCACTGCTCAATCTGTAATAACTGTGTGGAACGGTTTGACCATCACTATCCTTGGGTTGGGCAGTGTATTGGGCTAgtatgttg-----gatctt--ttgtctcc-tagtgttattttatt----------cttttttcttttttgtgtgaag-aatgttttgggggaa-------gagtagcttaatcccattgttaagtg---------------------------------------------------

upper sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA05G38360.1 (Glycine max), 5'ss of exon 3
GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgctagct--gttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttgaatt--gatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaacatatttgtgcag
||| ||| |||| |  ||    || || |||||  | ||  ||||||| ||||| || |||||||||||||| |||||||| || ||||| || ||||||||||    |      |  || ||     || || |  |||    |  |  | |  |  | | |  |||||  | |  |||  |||  | | |  |    |                                                                                
GCTCTACAGACCCCTCCGTGCTTCTCATTGTTCAGTCTGTGATAACTGCGTGGAGCGATTTGATCATCACTGCCCATGGGTTGGTCAGTGTATTGGACTGgtaacaaccattctttcataacttcacatttatggtatccaaggaacactatacacaggttatatacatagccctagattccgatactggcatttgaatt--------------------------------------------------------------------------------

upper sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT5G41060.1 (Arabidopsis thaliana), 5'ss of exon 3
GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtg-tgcacatacacttgaattgatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaacatatttgtgcag
||| ||  |||| ||||| |||||||| ||||| |||||||| |||||||| ||| ||||||| ||||||||||| ||||| || || || || |  |  ||||||| |||| | |  | | | |  |     |||   | | | | | || ||    |  | ||  |     |   | |   |||| ||                                                                                       
GCTCTATAGACCGCCTCGCTGCTCACATTGTTCGATTTGCAACAACTGTGTAGAAAGGTTTGACCATCACTGTCCTTGGGTTGGTCAATGTATTGCTCAAgtaagtttctcg-gtttttcgttttcctgtc--cgttagtttctgacatcagtctatataattcatctcattctccttgggaatttgcag---------------------------------------------------------------------------------------

upper sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT3G26935.1 (Arabidopsis thaliana), 5'ss of exon 3
GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgctagctgttttaatagcgtccttatattaga-acaatcgcggtgtgcacatacacttgaattgatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaacatatttgtgcag
||| ||  | || ||||| ||||| || || || |||||||| ||||| || ||| ||||||| |||||||| || ||||||||||| || || ||  ||||||||    | | || | | |||     ||  |||| |||   ||   |||    |  |     | || |  | |  | || ||  || |   | || | |                                                                           
GCTCTATAGGCCGCCTCGCTGCTCGCATTGCTCAATTTGCAACAACTGCGTAGAAAGGTTTGACCATCACTGCCCTTGGGTCGGCCAATGTATTGGGATGgtaagt----caaaat-ccaactg-----atcccgtctttaagctatccacataaaccatagtttcctaaatatcatctcatattctgatg-gttgttgcag---------------------------------------------------------------------------

upper sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv14s0068g01530.t01 (Vitis vinifera), 5'ss of exon 3
GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttga-attgatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaacatatttgtgcag
||| ||  |||| ||||| ||||||||||||||||| || |||||||| || ||||| |||||||| ||||| || ||||| || ||||| || ||||||||||       |||||   |  | |||||           ||||| ||   || ||  | |   || | |  | | ||| |           ||  ||  ||||  |  |                                                                   
GCTTTATAGACCTCCTCGCTGCTCACACTGTTCCATATGTAATAACTGCGTCGAACGATTTGATCACCACTGCCCTTGGGTTGGGCAGTGTATTGGACTGgtaa-------gagata--aattattttagaccttatgacatattggatgtatagcc-tatatccaaagaagtaacatttacaaaactcaacaccattcatggggtgggt-------------------------------------------------------------------

upper sequence: GRMZM5G821611_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv17s0000g00800.t01 (Vitis vinifera), 5'ss of exon 3
GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttactcgagatgctagctgttttaatagcgtccttatattagaacaatcgcggtgtgcacatacacttgaattgatgtttggaggtactctttctgggtagattttcatttttttaagttgttgactaactttctattctgttaagcctgatcatcaacatatttgtgcag
||| ||  |||| ||||| || ||||||||||| || |||||||| ||||||||||| ||||| |||||||| || ||||| || || || || ||||||||||  |   |    |  || |||| | |   || | || |   || |  ||| ||  |   || ||||      || |     | ||  |  | | | |                                                                            
GCTTTATAGACCTCCTCGCTGTTCACACTGTTCAATATGCAATAATTGTGTGGAACGATTTGACCATCACTGCCCTTGGGTTGGTCAATGTATTGGACTGgtaa--tgaacattcttttaactgtatcacatgctttctaaatgtaaattaat-gccattgacaaatactgcattatgggaacctagatttgttgtctttatt-------------------------------------------------------------------------

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|9255011|gb|BE345479.1|BE345479
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGGTCTTTTATATGTTTGGATTCTCGACGACATTGCTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttact ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC
EST: gi|60348094|gb|DN215067.1|DN215067
EST:     CATGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC
genomic: CATGGGTCGGCCAGTGCATAGGACTGgtaagttact ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC
EST: gi|60356386|gb|DN223359.1|DN223359
EST:     CATGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC
genomic: CATGGGTCGGCCAGTGCATAGGACTGgtaagttact ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC
EST: gi|89758330|gb|DY687546.1|DY687546
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttact ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC
EST: gi|149087864|gb|EE177142.2|EE177142
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttact ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC
EST: gi|71313270|gb|DR793166.1|DR793166
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttact ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC
EST: gi|19350925|gb|BM895457.1|BM895457
EST:     TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTG                         CGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC
genomic: TGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttact ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGC

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), 49 (downstream exon)
Score: 127

GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttact ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGCCTCTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 169

GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttact ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGCCTCTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttact ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGCCTCTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 213

GCTGTACCGACCACCTCGATGCTCACACTGTTCCATTTGCAATAACTGTGTGGAACGGTTTGATCATCACTGTCCATGGGTCGGCCAGTGCATAGGACTGgtaagttact ... atttgtgcagCGTAATTATCGGTTCTTCTATATGTTTGTATTCTCGACGACATTGCTCTGCCTCTATGTATTTGCCTTCTGTTGGGTGTATGTGATCAAGATTAGAGCTG