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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaaccccccataactctccctaacattttatccttttgtctggcaaagttgagaacttgtatgaaggattgggaatatgtgcagttatttatgga...

Basic information

species Zea mays
transcript GRMZM2G165418_T04
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 5'ss of exon 8
ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaaccc--cccataactctccc---taacattttatccttttgt-ctggcaa-agttgagaacttgtatgaaggattgggaatatg---tgcagttatttatgga------------------------------------------------------------
| ||| | ||||||||||||||||||||||| ||||||||||||||||||||||| ||||||||||| ||||||||  |||||||||||||||| || ||||||||||  |  |  ||  || |  |    |||||||||||| | ||| ||||    ||| | | |||| | |  | | |||||| |  |   ||||     || |  |                                                            
ACCCAACTCATTGTAATACACTGGCCTATAGCAGTTCAAAGGGTTCTATCCGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGATgttagtaattcatcttatgccttttacctgcaacattttatccgtgtgtactggaggtagtcgtggacttcttttgacggttgggacttggggctgcataagattctctattctatactagtaatagaatgtcacaatatcagcatgagataacaagaacctttaaacag

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA08G20830.2 (Glycine max), 5'ss of exon 8
ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttag-taacccccca----------taactctccctaacattttatccttttgtctggcaaagttgagaacttgtatgaaggattgggaatatgtgcagttatttatgga
| ||  | |||||||||||| |||| ||||| |||||||||||||| || || ||| ||||  |||| || |||||| | |||||    ||| | ||| ||| || | ||                |   | ||| ||    ||   |||      |  ||||||||||    |    |||  |||      | ||  |            
ACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGGCAGTCAGCATTATGTGATTCTCATGCCAAACTgtaagcttacattttgcttatgttatttgttttccttatggcttacacctaacaagtaacaaagttgaggttattggggaaaaattaaagggaagtagat-----------

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA15G02640.1 (Glycine max), 5'ss of exon 8
ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacccccc-----ataactct------ccctaacattttatccttttgtctggcaaagttgagaacttgtatgaaggattgggaatatgtgcagttatttatgga
| ||  | |||||||||||  |||| ||||| |||||||||||||| || || ||| ||||  |||| ||||||||| | |||||    ||| | ||| ||| ||||    |       ||||   |       ||| |||  |   || ||  ||    || | |   |  || ||  ||   ||   |   |   |||           
ACCCTACACATTGTAATACGTTGGCATATAGCAGTTCAAAGGGTTCAATTCGTCTTGTTGACTTGCGACAATCAGCATTATGTGATTCTCATGCTAAACTgtaagtacattcttttgttataatcttgttggttcctgacaagtatcccattcctcccataaggctttcagattttaacaaatgtttaaacagttgacag-----------

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA13G42800.1 (Glycine max), 5'ss of exon 8
ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaaccccccataactctccctaacattttatccttttgtctggcaaagttgagaacttgtatgaaggattgggaatatgtgcagttatttatgga-------
| ||  | |||||||||||| |||| ||||| |||||||||||||| ||||| ||| ||||  |||| ||||||||| | |||||    ||| | ||| ||| ||||    |   |     |  ||   |||   ||||   |  |     |    |   ||   || | |  ||  |    | | ||| | || |   |       
ACCCTACACATTGTAATACATTGGCATATAGCAGTTCAAAGGGTTCAATCCGTCTTGTTGACTTGCGGCAATCAGCATTATGTGATTCTCATGCCAAACTgtaagtacattcttttgtggttatct--tattcgttcctgacgaataa-gtatcccattcctcccataaggctttcag----tcttcagattttaacaaatgttgaa

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 8
ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaac-cccccataactctccctaacattttatccttttgtctggcaaagttgagaacttgtatgaaggattgggaatatgtgcagttatttatgga-----------------------------------------------------------------------------------------
||||   |||||||||||  || || |||||||||||||| || || || ||  | |||||| ||||||||||||| ||||||||    ||| | ||| ||| |||      | ||| |  ||   |   |  |  |  ||   | |  |||   |    ||||  |  | ||  |  ||||| |||   | ||||                                                                                              
ATCCTATCCATTGTAATATGCTCGCATATAGTAGTTCAAAAGGCTCCATTCGTTTGATTGATATGCGTCAATCAGCTCTGTGTGATTCTCATACGAAATTgtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaa---tatatactta-agaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacag

upper sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 8
ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaaccccccataactctccctaacattttatccttttgtctggca-aagttgagaacttgtatgaaggattgggaatatgtg-cagttatttatgga
| ||  |||||||||| |   | || |||||||||||||| || || ||||| |||| |||| |||| || ||||||||||||||    ||||| ||| ||| |||  |   |  |   | |    |   || | |  |||  | || |  ||  | | |   |   |||||||  |  |  |  || || |    ||    
ACCCTACCCATTGTAACATGTTAGCATATAGTAGTTCAAAAGGCTCAATCCGCCTTAATGATTTGCGACAGTCAGCACTGTGTGATTCTCATTCTAAATTgtgagtggcttgc--ttgttttagtcatttttattttttttcatttgtcttaaaataatataataggtgaaggagagaaatcaaatggcaatagaataactc

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|31352864|gb|CD437221.1|CD437221
EST:     CGACTTATTGATCTGCGCCAATCAGCACTGTGTGACAACCATTCAAAAAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST: gi|211384024|gb|FL015619.1|FL015619
EST:     CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST: gi|24934206|gb|CA452424.1|CA452424
EST:     CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST: gi|211386654|gb|FL015627.1|FL015627
EST:     CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST: gi|211386649|gb|FL015622.1|FL015622
EST:     CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST: gi|67025874|gb|CO454623.1|CO454623
EST:     CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT

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: 168

ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 152

ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 167

ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT