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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttcccacttcccctccctccctcgcggcctcgccgtctcgccctttccttcgtcctcacctgctttttatcgccctaatctgaacgcgctcttgt...

Basic information

species Zea mays
transcript GRMZM2G089259_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089259_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g07912.1 (Oryza sativa), 5'ss of exon 2
TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgt-tcccacttcccctccctccctcgcggcctcgccgtctcgccctttccttcgtcctcacctgctttttatcgccctaatctgaacgcgctcttgt
|||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||  || |   |  |      ||  ||   |  |  |  |   |   | | | | |     | |      |  | | ||   | |||| |   |   |  |
TGGCTGCGCAAGACGAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgttagtatagtaacttagtaaccagccaatcaccaccttcagttgttcatctgcgtaaaagtaattcatgtaattttgcag-actctgtaactgtcgtctt
















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|74237070|gb|DT644984.1|DT644984
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|50337271|gb|CO532397.1|CO532397
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|211183324|gb|FK979377.1|FK979377
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|87157614|gb|DY402403.1|DY402403
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|71428557|gb|DR809607.1|DR809607
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|94475718|gb|EB704676.1|EB704676
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|211180921|gb|FK979369.1|FK979369
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGNCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|50336816|gb|CO531942.1|CO531942
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|211183319|gb|FK979372.1|FK979372
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|211180923|gb|FK979371.1|FK979371
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|211183323|gb|FK979376.1|FK979376
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCTAAG                         AGCTGATGCTGCTCGGAGTNATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|22546168|gb|BU098479.1|BU098479
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|71321201|gb|DR797302.1|DR797302
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|71329466|gb|DR801453.1|DR801453
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|211183322|gb|FK979375.1|FK979375
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|87157722|gb|DY402511.1|DY402511
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|148957093|gb|EC903064.2|EC903064
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|22819833|gb|BU499923.1|BU499923
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|37421156|gb|CF648275.1|CF648275
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|211226258|gb|FL422663.1|FL422663
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|211183328|gb|FK979381.1|FK979381
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|71428023|gb|DR809073.1|DR809073
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|76012907|gb|DT940077.1|DT940077
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|26558674|gb|CA830909.1|CA830909
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|211180922|gb|FK979370.1|FK979370
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|33466850|gb|CF243899.1|CF243899
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
EST: gi|148994788|gb|EE034233.2|EE034233
EST:     CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAG                         AGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT
genomic: CAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCT

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: 45 (upstream exon), 48 (downstream exon)
Score: 59

TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCTTCATATCGGAGATCTGCGTGCCGTCCTCGCTCTTCACCAGCCGCTTCTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 25

TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCTTCATATCGGAGATCTGCGTGCCGTCCTCGCTCTTCACCAGCCGCTTCTA


Block sizes: 35 (upstream exon), 48 (downstream exon)
Score: 8

TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCTTCATATCGGAGATCTGCGTGCCGTCCTCGCTCTTCACCAGCCGCTTCTA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 56

TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttccc ... ctgcacgcagAGCTGATGCTGCTCGGAGTCATCTCGCTGCTGCTCAGCCAGACGGCGCGCTTCATATCGGAGATCTGCGTGCCGTCCTCGCTCTTCACCAGCCGCTTCTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCTGCGCAAGACCAAGCGGAAGGCCATGCTCGCCGCGCTCGAGAAGATCCGCGAAGgtacgttcccacttcccctccctccctcgcggcctcgccgtctcgccctttccttcgtcctcacctgctttttatcgccctaatctgaacgcgctcttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcgcc