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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagttaaacactactggtatctgtctttcccttcccttccatttataactttcaatgggtcatgaaatcattcacatttttgcttttgataacca...

Basic information

species Zea mays
transcript AC215690.3_FGT002
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC215690.3_FGT002 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g31070.1 (Oryza sativa), 5'ss of exon 2
CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagttaaacactact--ggtatc-tgtctttcccttcccttccatttataactttcaatgggtcatgaaatcattcacatttttgcttttgataacca------
||| |||||||| || ||||| ||||||||||||||||||||||| |||||||||||||||||||||||||| |||||||| |||||||| || || |||||||| || |||   ||| |  || ||  ||   ||   |||| ||  | ||| |  || |||||         ||  |  | |   ||| | |  ||| |||      
CAGGCATGGTGATCTTCTTAATAAGTACATGTACCTTACTGGACGTGTTGACATGAAACAAATTGAGAAGACAATACAATACCTGATTGGGTCTGGGATGgtaag-agctaatatctatttaggcatgatgatattattttcctttttactta-agtttacaatgct-------attgtggataaccttgttatcaatagccatgtctc

upper sequence: AC215690.3_FGT002 (Zea mays), 5'ss of exon 2
lower sequence: EFJ20436 (Selaginella moellendorffii), 5'ss of exon 1
CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagttaaacactactggtatctgtctttcccttcccttccatttataactttcaatgggtcatgaaatcattcacatttttgcttttgataacca
  | ||||| ||  | || ||||||||  | ||||| |||||||| || |||||||| ||||| |||||||| || || ||  |||| ||||| ||||||||||| ||   |          | || |    ||      |     ||     ||| ||                                         
TCGTCATGGCGATTTGCTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaag-agcagagtttcttctttctcgggaactcaaaagtcggtttttccattcttgcag----------------------------------------

upper sequence: AC215690.3_FGT002 (Zea mays), 5'ss of exon 2
lower sequence: EFJ28408 (Selaginella moellendorffii), 5'ss of exon 1
----------------------CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagttaaacactactggtatctgtctttcccttcccttccatttataactttcaatgggtcatgaaatc-------attcacatttttgcttttgataacca---------
                        | ||||||||  | || ||||||||  | ||||  |||||||| ||||||||||| ||||| |||||||| || || ||  |||| ||||| ||||||||||  ||  | |   |  |  |           ||     |  | |||  | | ||  | || || | | | |       || || || |  | ||    ||  |          
GTGCCTGGACTGCCGAGGAGAATCGCCATGGTGATTTGCTCAACAAGTATCTCTACCGCACTGGACGAGTTGACATGAAGCAAATCGAGAAGACGATCCAgtacttgatcggttctggaatggtaaagagccagagtttcttctttctcaggaactccaaagttcgcgtttccatccttgca-ggatcctcagaccgagaacaatccatatctcgggttcgtctacacgtccttccag

upper sequence: AC215690.3_FGT002 (Zea mays), 5'ss of exon 2
lower sequence: EFJ28417 (Selaginella moellendorffii), 5'ss of exon 1
CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagttaaacactactggtatctgtctttcccttcccttccatttataactttcaatgggtcatgaaatcattcacatttttgcttttgataacca
  | ||||||||  | || ||||||||  | ||||| |||||||| || |||||||| ||||| |||||||| || || ||  |||| ||||| ||||||||||| ||   |    | ||  | |||      | |     |||  ||| |   ||      |                                     
TCGCCATGGTGATTTACTCAACAAGTATCTCTACCTCACTGGACGAGTCGACATGAAGCAAATCGAGAAGACGATCCAGTACTTGATCGGTTCTGGAATGgtaag-agcccagagtttcttctttctcgggaactcaaaagttcggtttttccattcttccag-------------------------------------

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|32847096|gb|CD986777.1|CD986777
EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
EST: gi|74245141|gb|DT653055.1|DT653055
EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
EST: gi|93281940|gb|EB674204.1|EB674204
EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
EST: gi|18964949|gb|BM661303.1|BM661303
EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCC
EST: gi|60352849|gb|DN219822.1|DN219822
EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
EST: gi|18964947|gb|BM661302.1|BM661302
EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCC
EST: gi|32844409|gb|CD984090.1|CD984090
EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
EST: gi|74244362|gb|DT652276.1|DT652276
EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
EST: gi|32833577|gb|CD973255.1|CD973255
EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
EST: gi|32846330|gb|CD986011.1|CD986011
EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
EST: gi|32845620|gb|CD985301.1|CD985301
EST:     ACATGAAACAAATTGAGAAGACCATCCAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
EST: gi|18964155|gb|BM660842.1|BM660842
EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGNTCCGGAATG                         GATCCTGGAACTGAGAACAACCCC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCC
EST: gi|22542531|gb|BU092969.1|BU092969
EST:     ACATGAAACAAATTGAGAAGACCATACAACATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC
EST: gi|6626396|gb|AW257928.1|AW257928
EST:     ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATG                         GATCCTGGAACTGAGAACAACCCCTACTTGNGTTTCCTCTACACATCATTC
genomic: ACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTC

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: 457

CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTCCAAGAAAGGGCAACATTTGTGTCGCATGGGAATACTGCAAGGCATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 649

CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTCCAAGAAAGGGCAACATTTGTGTCGCATGGGAATACTGCAAGGCATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 584

CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTCCAAGAAAGGGCAACATTTGTGTCGCATGGGAATACTGCAAGGCATGCCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1451

CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagtt ... tcttatgcagGATCCTGGAACTGAGAACAACCCCTACTTGGGTTTCCTCTACACATCATTCCAAGAAAGGGCAACATTTGTGTCGCATGGGAATACTGCAAGGCATGCCA


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGACATGGTGACCTCCTTAACAAGTACATGTACCTTACTGGACGGGTTGACATGAAACAAATTGAGAAGACCATACAATATCTGATTGGTTCCGGAATGgtaagcagttaaacactactggtatctgtctttcccttcccttccatttataactttcaatgggtcatgaaatcattcacatttttgcttttgataacca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccttccc