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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccctgtcatcgaatcttagaactgaaactatggttttcaagtaagacccgttcgtttttctgacaatatcttgcacactttgtttcag

Basic information

species Zea mays
transcript GRMZM2G075978_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G075978_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os02g55410.2 (Oryza sativa), 5'ss of exon 16
AGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccctgtcatcgaatcttagaactgaaactatggttttcaagtaagacccgttcgtttttctgacaatatcttgcacactttgtttcag
||| |||||||||||||||||||| ||||| || || |||||||||||||||||||| ||||| ||||| |||||  |||||||||||||||||||||| ||  | | ||||||||   || ||   | | ||   || | |||  ||||        || ||||||| |   || | | |      || |||||
AGCTGAGGCACAAATAAAGAGAAGGATGGGAATTGGAAGCCACATATCCGAGCGACGCCTGATCGATGAACTAAATAGGATGGGGATGAATGAATCCATTgtgaggaacctgtcatactat-ttgctatttaattaattgattt--agta--------tcatttttcttatgctaccattcgg---ctgcttcag

upper sequence: GRMZM2G075978_T01 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA13G22420.1 (Glycine max), 5'ss of exon 17
AGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccctgtcatcgaatcttagaactgaaactatggttttcaagtaagacccgttcgtttttctgacaatatcttgcacactttgtttcag----------
||| ||  | || |||||||||||||| || || || | ||||||||| ||  || ||||||||||||| || | | | ||||||||||||||||| || ||| | |||   |   |    ||||  || ||||  ||||| |   ||   |      |   |||  || ||  |  | |  |    | ||  |           
AGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTATTgtaagtaccaaatagcca---ctta--acggaaaagatggtctcatagcttgtaatcctgaatttgatgtcaccacttggttccaacttttaaaagatgcacgtt

upper sequence: GRMZM2G075978_T01 (Zea mays), 5'ss of exon 18
lower sequence: GLYMA17G11220.1 (Glycine max), 5'ss of exon 17
AGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccctgtcatcgaatcttagaactgaaactatggttttcaagtaagacccgttcgtttttctgacaatatcttgcacactttgtttcag----------
||| ||  |||| |||||||||||||| || || || | ||||||||| ||  || ||||||||||||| || | | | ||||||||||||||||| || ||| |  ||   |   |    ||||  |||||||  ||||| |   ||          |   |||| || ||  |  | |  |    | ||  |           
AGCTGAAACACAGATAAAGAGAAGAATTGGAATTGGAAACCACATATCGGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTATTgtaagttccaaatagcca---ctta--actgaaaagatggtctcatagcttataaacctgaattttatgtcaccacttggttccaacttttaaaagatgcacgtt

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|67015692|gb|CO444441.1|CO444441
EST:     AGCGACGGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|12969601|gb|BG266545.1|BG266545
EST:     GCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: GCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|76933303|gb|DV173407.1|DV173407
EST:     AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|211443723|gb|FK945773.1|FK945773
EST:     AGCGACGGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGC
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGC
EST: gi|14191099|gb|BG833329.1|BG833329
EST:     AGCGACGGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGC
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGC
EST: gi|4804371|gb|AI666237.1|AI666237
EST:     AGCGACGGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|211443724|gb|FK945774.1|FK945774
EST:     AGCGACGGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|5468730|gb|AI834521.1|AI834521
EST:     AGCGACGGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|76933305|gb|DV173408.1|DV173408
EST:     AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|78544713|gb|DV622211.1|DV622211
EST:     AGCGACGGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|166614915|gb|EG155686.1|EG155686
EST:     ATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: ATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|4966494|gb|AI691350.1|AI691350
EST:     AGCGACGGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|71771846|gb|DR969783.1|DR969783
EST:     AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|211441601|gb|FK945768.1|FK945768
EST:     AGCGACGGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|211441600|gb|FK945767.1|FK945767
EST:     AGCGACGGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|22546223|gb|BU098534.1|BU098534
EST:     AGCGACTGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCC-TTCTG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTG
EST: gi|71435361|gb|DR816411.1|DR816411
EST:     AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|211441604|gb|FK945771.1|FK945771
EST:     AGCGACGGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|166586066|gb|EG269453.1|EG269453
EST:     AGCGACGGCTGATTGATGAGCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCA
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCA
EST: gi|4572954|gb|AI586603.1|AI586603
EST:     AAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|71429881|gb|DR810931.1|DR810931
EST:     AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
EST: gi|149000776|gb|EE037999.2|EE037999
EST:     AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATC                         GTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG
genomic: AGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAG

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), 48 (downstream exon)
Score: 99

AGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAGAGAGAGCGCCACGTGATCGTCCGAAAGGCTTGAGGTGGAGAGGCCAGTC


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 24

AGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAGAGAGAGCGCCACGTGATCGTCCGAAAGGCTTGAGGTGGAGAGGCCAGTC


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 17

AGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAGAGAGAGCGCCACGTGATCGTCCGAAAGGCTTGAGGTGGAGAGGCCAGTC


Block sizes: 47 (upstream exon), 27 (downstream exon)
Score: 3

AGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccc ... tttgtttcagGTCAGAAGAGCCCTTCTGATCATGCATCAAAGGGACGAGGTGGAGTACAAGAGAGAGCGCCACGTGATCGTCCGAAAGGCTTGAGGTGGAGAGGCCAGTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCATCgtaggaaccctgtcatcgaatcttagaactgaaactatggttttcaagtaagacccgttcgtttttctgacaatatcttgcacactttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT