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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGAAGACTTGAGGCAGCTTTGTGCTGACCCTAGAGCAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctcttctgctctgacccacgtagcaaattctaaatgttcaatccaagcgaaactcttgtgctgtgatgatttatattggtcttctgtgcccag

Basic information

species Zea mays
transcript GRMZM2G176546_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os12g04990.2 (Oryza sativa), 5'ss of exon 21
TGCGAAGACTTGAGGCAGCTTTGTGCTGACCCTAGAGCAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctcttctgctctgacccacgtagcaaattctaaatgttcaatccaagcgaaactcttgtgctgtgat-gatttatattggtcttctgtgcccag
  ||| || || || |||||||||||||| || | ||||||| |||| |||||||| || ||||| ||| |||| ||||||||||||||||   |||    ||       || | |||   ||| |||     ||  || |     | |  | |  | ||  || | | ||    | |||  ||   
CACGAGGATTTAAGACAGCTTTGTGCTGATCCGAAAGCAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttctc--acttctcataaccttgcatgctcttaataagttatg-aatcatgtgtatgattcccttattaatctctctttccttgctgcaccag-

upper sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os11g04980.2 (Oryza sativa), 5'ss of exon 21
TGCGAAGACTTGAGGCAGCTTTGTGCTGACCCTAGAGCAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctcttctgctctgacccacgtagcaaattctaaatgttcaatccaagcgaaactcttgtgctgtg---atgatttatattggtct-tctgtgcccag------------
| ||| || || || ||||| || |||||  | || ||||||||||| |||||||| |||||||| ||| |||| ||||| ||||||||||   | |       |    |       | || ||      | |||  |||  ||| |  |||    ||   |||||   |||   ||| |||||||  |             
TACGAGGATTTAAGACAGCTATGCGCTGATACAAGGGCAAGAGCTGCTGTCCTGGCTGACATGGACTCTATTGGAAAGGAGGCACAGgtttaattttcacttcttagttcttaccttacatgct---ctcttaat--aagtaaaagttctgtatgatgtgtatgatccttatctatctctctgtgcttacttactgtaccag
















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|6194573|gb|AW146677.1|AW146677
EST:     CAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTC
genomic: CAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctct ... ctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTC
EST: gi|67023162|gb|CO451911.1|CO451911
EST:     CAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTNGGGAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTC
genomic: CAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctct ... ctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTC
EST: gi|50335867|gb|CO530993.1|CO530993
EST:     GTTGGGAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTC
genomic: GTTGGGAAGGAAGCACAGgtttctctct ... ctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTC
EST: gi|78023366|gb|DV491753.1|DV491753
EST:     CAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTC
genomic: CAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctct ... ctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTC
EST: gi|93281969|gb|EB674233.1|EB674233
EST:     CAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTC
genomic: CAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctct ... ctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTC
EST: gi|6194494|gb|AW146598.1|AW146598
EST:     CAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCC
genomic: CAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctct ... ctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCC
EST: gi|5915188|gb|AW052829.1|AW052829
EST:     CAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTC
genomic: CAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctct ... ctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTC

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), 47 (downstream exon)
Score: 63

TGCGAAGACTTGAGGCAGCTTTGTGCTGACCCTAGAGCAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctct ... ctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTCACAGTGGACAATGGTCTCCTCACCCCAACATTCAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 223

TGCGAAGACTTGAGGCAGCTTTGTGCTGACCCTAGAGCAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctct ... ctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTCACAGTGGACAATGGTCTCCTCACCCCAACATTCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 275

TGCGAAGACTTGAGGCAGCTTTGTGCTGACCCTAGAGCAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctct ... ctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTCACAGTGGACAATGGTCTCCTCACCCCAACATTCAAG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 87

TGCGAAGACTTGAGGCAGCTTTGTGCTGACCCTAGAGCAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctct ... ctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTCACAGTGGACAATGGTCTCCTCACCCCAACATTCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGAAGACTTGAGGCAGCTTTGTGCTGACCCTAGAGCAAGAGCTGCAGTCCTGGCCGACATGGATTCTGTTGGGAAGGAAGCACAGgtttctctcttctgctctgacccacgtagcaaattctaaatgttcaatccaagcgaaactcttgtgctgtgatgatttatattggtcttctgtgcccag

- - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA