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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGGAGATAATCAAATACAAGGGCTTCCAAGTACCTCCTGCGGAGCTTGAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgatccgcactgaaatcctgagatggcattaagccgcatggtccacatcgctttggtgtcgaggaattaatacttttggatcaattgcag

Basic information

species Zea mays
transcript GRMZM2G055320_T03
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G055320_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os06g44620.1 (Oryza sativa), 5'ss of exon 4
TGAAGGAGATAATCAAATACAAGGGCTTCCAAGTACCTCCTGCGGAGCTTGAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgatccgcactgaaatcctgagatggcattaagccgcatggtccacatcgctttggtgtcgaggaattaatacttttggatcaattgcag
| ||||| ||||| ||||||||||| |||||||||||||||||||| |||||||| |||||||||||||| ||||| ||||||||||| || |||||  |||||||||||||   || | ||    ||| ||       | ||||| ||||  || | |  |     |||| | ||| ||| | ||    ||||||
TCAAGGAAATAATAAAATACAAGGGGTTCCAAGTACCTCCTGCGGAACTTGAAGCTCTTCTCATCACACACCCTGATATCAAGGATGCTGCCGTTGTACCgtaagttgatccatgcttagatgaacagaaggt------cagcatgttcca--tcacatcag-----aggactaaattcttattgaattcttgcag
















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|211370703|gb|FL471723.1|FL471723
EST:     AAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: AAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|211365922|gb|FL274320.1|FL274320
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|14242682|gb|BG840387.2|BG840387
EST:     ACATCCTGAAAT-AAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: ACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|14202260|gb|BG835937.1|BG835937
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|211365921|gb|FL274319.1|FL274319
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCG
EST: gi|4826223|gb|AI667851.1|AI667851
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|211119687|gb|FL454266.1|FL454266
EST:     GATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: GATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|211033456|gb|FL445334.1|FL445334
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|211365924|gb|FL274322.1|FL274322
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGMTGTTGTCTC                         GATGAAAGATGAAGTCKCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|211082093|gb|FL165107.1|FL165107
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGC-GGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|76911495|gb|DV164298.1|DV164298
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|211365923|gb|FL274321.1|FL274321
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGGCGAAGTCCCGG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGG-CGAAGTCCCGG
EST: gi|28984816|gb|BQ539233.2|BQ539233
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|45568106|gb|CK985905.1|CK985905
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCCGTGGCATTCATTATACGCAG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|67019027|gb|CO447776.1|CO447776
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCCGTGGCATTCATTATACGCAG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|148978851|gb|EE026338.2|EE026338
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCCCCGGCGAAGTCCCGGTGGGCATTCATTATACGCA
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGG-CATTCATTATACGCA
EST: gi|7958402|gb|AW862704.1|AW862704
EST:     AAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCGTGGTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCA
genomic: AAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGC-TGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCA
EST: gi|211082094|gb|FL165108.1|FL165108
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATA
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATA
EST: gi|149000216|gb|EE037361.2|EE037361
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
EST: gi|76924614|gb|DV170050.1|DV170050
EST:     GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTC                         GATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG
genomic: GAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAG

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), 47 (downstream exon)
Score: 24

TGAAGGAGATAATCAAATACAAGGGCTTCCAAGTACCTCCTGCGGAGCTTGAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAGTGAAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 138

TGAAGGAGATAATCAAATACAAGGGCTTCCAAGTACCTCCTGCGGAGCTTGAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAGTGAAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAG


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

TGAAGGAGATAATCAAATACAAGGGCTTCCAAGTACCTCCTGCGGAGCTTGAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAGTGAAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 619

TGAAGGAGATAATCAAATACAAGGGCTTCCAAGTACCTCCTGCGGAGCTTGAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgat ... tcaattgcagGATGAAAGATGAAGTCGCCGGCGAAGTCCCGGTGGCATTCATTATACGCAGTGAAGGCTCTGAGATCAGTGAGAACGAGATCAAGCAGTTTGTTGCAAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGGAGATAATCAAATACAAGGGCTTCCAAGTACCTCCTGCGGAGCTTGAAGCCCTTCTCATCACACATCCTGAAATCAAGGATGCCGCTGTTGTCTCgtaagttgatccgcactgaaatcctgagatggcattaagccgcatggtccacatcgctttggtgtcgaggaattaatacttttggatcaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT