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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATGGCGTGCTTTGATGGATGAGATGGCTATCGTCGCCACAAAGGAATACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttcacttttctttgctcgtgttttctcttttctagacaccttcacttgtctttatattgtttgtgcaattaccactatgagagcttggttgta...

Basic information

species Zea mays
transcript GRMZM2G110714_T02
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110714_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 5'ss of exon 10
AGAATGGCGTGCTTTGATGGATGAGATGGCTATCGTCGCCACAAAGGAATACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttcacttttctttgctcgtgttttctctttt----ctagacaccttcacttgtctttatattgtttgtgcaattaccactatgagagcttggttgta
|||||||||||||||||||||||| |||||    || || ||||| ||||||||||| || || ||  | ||  | || ||||||||||| ||||||||||||||| |||  ||||   |        ||| | ||||     || | |  | |  ||   |||| |   ||| |||  |      |   | ||||   ||| |
AGAATGGCGTGCTTTGATGGATGAAATGGCCGCTGTTGCTACAAAAGAATACCGGTCCATTGTCTTCCAAGAGGCACGATTTGTTGAATATTTCCGCCTTgtaagtattctttttttaataacttcagtttttgttttatgcttataaaaatactgttcattttaaaccttttatgctgtc----ttgaaatagctatcttgaa

upper sequence: GRMZM2G110714_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA13G34560.1 (Glycine max), 5'ss of exon 9
AGAATGGCGTGCTTTGATGGATGAGATGGCTATCGTCGCCACAAAGGAATACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttcacttttctttgctcgtgttttctcttttctagacaccttcacttgtctttatattgtttgtgcaattaccactatgagagcttggttgta-------
|||||||||||||||||||||| |||||||| || | || ||  |||||||||| || || |||||  ||||||| ||||||||||| || |||||||| ||||| |  ||| |||  |        |  |    |   ||  ||  || | || |  | | ||    || |   |||        | | |||| ||||        
AGAATGGCGTGCTTTGATGGATCAGATGGCTGTCATTGCTACTGAGGAATACCGTTCCATTGTATTCAAGGAACCACGCTTTGTTGAGTATTTCCGCCTGgtaag-gaccacatttagtaaacaacttaattaagtacttattca--ttaagttcttatcagatgacatgagaccttatt----caaaaacttgattgtgaaacttg

upper sequence: GRMZM2G110714_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA12G35840.1 (Glycine max), 5'ss of exon 8
AGAATGGCGTGCTTTGATGGATGAGATGGCTATCGTCGCCACAAAGGAATACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttcacttttctttgctcgtgttttctcttttctagacaccttcacttgtctttatattgtttgtgcaattaccactatgagagcttggttgta-------
|||||||||||||||||||||| |||||||| || | || ||  |||||||||| || || |||||  ||||||| ||||||||||| || |||||||| ||||| |  ||| |||  |        |  ||   |   ||  ||  || | || |  | | ||    | ||   ||   | ||    | |||| ||||        
AGAATGGCGTGCTTTGATGGATCAGATGGCTGTCATTGCTACTGAGGAATACCGTTCCATTGTATTCAAGGAACCACGCTTTGTTGAGTATTTCCGCCTGgtaag-gaccacatttagtaaacaacttaatcaagtacttattca--ttgagttcttatcagatgacatatgagcttgttaata----aacttgattgtgaaacatg

upper sequence: GRMZM2G110714_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA06G33380.1 (Glycine max), 5'ss of exon 8
AGAATGGCGTGCTTTGATGGATGAGATGGCTATCGTCGCCACAAAGGAATACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc------acttttctttgctcgtgttttctcttttctagacacct-tcacttgtctttatatt-gtttgtgcaattaccactatgagagcttggttgta
||||||||| ||||||||||||||||||||| || | |||||  |||| |||||||| || || ||  | ||||| || |||||||| || |||||||| |||||  | |      | ||   ||   |    ||||   |  | || | |  | |      | || || || ||||||| ||       | |||  | |        
AGAATGGCGGGCTTTGATGGATGAGATGGCTGTCATTGCCACTGAGGAGTACCGGTCCATTGTGTTCAAAGAACCACGATTTGTTGAGTATTTCCGCCTGgtaaggttactacaggaattggtttaaatttatttttaattcctataaataaatattgtgaattttgattttagtttgtgtaaaatgttttttgatggtt--------

upper sequence: GRMZM2G110714_T01 (Zea mays), 5'ss of exon 8
lower sequence: GLYMA20G09810.1 (Glycine max), 5'ss of exon 9
AGAATGGCGTGCTTTGATGGATGAGATGGCTATCGTCGCCACAAAGGAATACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttcactt----ttctttgctcgtgttttctcttttc-tagacaccttcacttgtctttatattgtttgtgcaattaccactatgagagcttggttgta
 |||||| | ||||||||||||||||||||| || | |||||  |||| |||||||| || || ||  | ||||| || |||||||| || |||||||| |||||  | |        ||  ||     ||||||  ||| |  || | |   | | || |  || || |    ||  |||      | |  |   |||||    
GGAATGGAGGGCTTTGATGGATGAGATGGCTGTCATTGCCACTGAGGAGTACCGGTCCATTGTGTTCAAAGAACCACGATTTGTTGAGTATTTCCGCCTGgtaaggttcctacagaaattggttaaatatgtttttacttcttataaatatggtgaattttgattttagttcgggtaaaatgttttttgtt-ggttttggt----

upper sequence: GRMZM2G110714_T01 (Zea mays), 5'ss of exon 8
lower sequence: Vv12s0028g02180.t01 (Vitis vinifera), 5'ss of exon 8
AGAATGGCGTGCTTTGATGGATGAGATGGCTATCGTCGCCACAAAGGAATACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttcacttttctttgctcgtgttttctcttttctagacaccttcacttgtctttatattgtttgtgc-aattaccactatgagagcttggttgta-
||||||||||||  | ||||||||||||||| || | ||||| |||||||| || || || || ||  ||||||| |||||||||||||| |||||||| |||||| |     | | | | |     | ||     |   |||     |   |  ||  ||   | | || |   ||   |   ||   || | | | ||  
AGAATGGCGTGCACTCATGGATGAGATGGCTGTCATTGCCACCAAGGAATATCGTTCCATTGTCTTCCAGGAACCCCGCTTTGTTGAATATTTCCGCCTGgtaagtttgattatatttctaccaacttcttggaggtctcagaa--tgttgttgatcaatagcatatatgagttgatcttctgcattctagatcgatagttc

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|211502934|gb|FL212597.1|FL212597
EST:     ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTT                         GCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
genomic: ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
EST: gi|211505276|gb|FL212599.1|FL212599
EST:     ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTT                         GCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
genomic: ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
EST: gi|211505277|gb|FL212600.1|FL212600
EST:     ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTT                         GCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
genomic: ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
EST: gi|26457670|gb|CA829253.1|CA829253
EST:     ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATATTTCCGCCTT                         GCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
genomic: ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
EST: gi|211502933|gb|FL212596.1|FL212596
EST:     ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTT                         GCAACGCCMGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
genomic: ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
EST: gi|60353908|gb|DN220881.1|DN220881
EST:     ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTT                         GCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG
genomic: ACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCG

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: 185

AGAATGGCGTGCTTTGATGGATGAGATGGCTATCGTCGCCACAAAGGAATACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCGAAAAGAAAGCCGAGTGCGGGCATCGAGTCGCTGCGCGCAATCCCTTGGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 116

AGAATGGCGTGCTTTGATGGATGAGATGGCTATCGTCGCCACAAAGGAATACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCGAAAAGAAAGCCGAGTGCGGGCATCGAGTCGCTGCGCGCAATCCCTTGGA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 57

AGAATGGCGTGCTTTGATGGATGAGATGGCTATCGTCGCCACAAAGGAATACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCGAAAAGAAAGCCGAGTGCGGGCATCGAGTCGCTGCGCGCAATCCCTTGGA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 123

AGAATGGCGTGCTTTGATGGATGAGATGGCTATCGTCGCCACAAAGGAATACCGGTCAATCGTATTTGAGGAACCGCGCTTTGTTGAATACTTCCGCCTTgtaagtgttc ... tttgaaacagGCAACGCCAGAGATGGAGTATGGCAGGATGAACATCGGAAGCAGGCCATCGAAAAGAAAGCCGAGTGCGGGCATCGAGTCGCTGCGCGCAATCCCTTGGA