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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatgtgttgacagtctaggcgtcctctccaccattgcgctgatggttgcttattaggtatgtcatgatgtgctttcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGTCCATAGGTCCAGGAATAAGCAAGGGTGCGCCCTCCTCCGAACACGCACT

Basic information

species Zea mays
transcript GRMZM2G081682_T02
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G081682_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os07g47290.3 (Oryza sativa), 3'ss of exon 18
---------------gtaaatgtgttgacagtctaggcgtcctctc--caccattgcgctgatggttgcttatt---aggtatgtcatgatgtgctttc-ctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCA---TGTCCATAGGTCCAGGAATAAGCAAGGGTGCGCCCTCCTCCGAACACGCACT-
                || | |  || |   ||   |  |  |      | | ||| | ||||| ||||| |||   |  | ||   | ||||| |||| |  | ||||||||||| ||||||||||||||  |||| ||||||||| ||  |      ||| ||||| || ||||||||      |  |||| |     | | ||| | | 
gtaactggaattataatatacgcatttaacttcatagtataatagaaatatctttgggttgatgattgctcatttttaactttgctttcatgtgatttctcaatacagGAACTGGCTGAGATTCTGTTCCAAGCTGCTCTATAGATGGTGCCGTGGTGCTGTTCATAGTTCTAGGAATAAAGCCTAGCACGCCTTT----GGAAACGGAATG
















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|21389890|gb|BQ527939.1|BQ527939
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|33101487|gb|CF061447.1|CF061447
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|6466763|gb|AW191423.1|AW191423
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCCCTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|5739589|gb|AI947384.1|AI947384
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCCCTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|60347665|gb|DN214638.1|DN214638
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTCCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|21331635|gb|BQ487016.1|BQ487016
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|32909378|gb|CF014190.1|CF014190
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|22715088|gb|BU197571.1|BU197571
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCCCTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCCGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|60397236|gb|DN230052.1|DN230052
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|6095640|gb|AW120307.1|AW120307
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCCCTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGCCCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|166552970|gb|EG247183.1|EG247183
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTC
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTC
EST: gi|16926966|gb|BM080034.1|BM080034
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|166450987|gb|EG077507.1|EG077507
EST:     AAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATACCGGTCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCC
genomic: AAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCAT-CCGG-CAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCC
EST: gi|9794851|gb|BE553159.1|BE553159
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|5804468|gb|AI979438.1|AI979438
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCCCTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|74237144|gb|DT645058.1|DT645058
EST:     AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: AAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
EST: gi|60350641|gb|DN217614.1|DN217614
EST:     GGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAG                         GAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT
genomic: GGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGT

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), 49 (downstream exon)
Score: 242

GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGTCCATAGGTCCAGGAATAAGCAAGGGTGCGCCCTCCTCCGAACACGCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 252

GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGTCCATAGGTCCAGGAATAAGCAAGGGTGCGCCCTCCTCCGAACACGCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 155

GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGTCCATAGGTCCAGGAATAAGCAAGGGTGCGCCCTCCTCCGAACACGCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 262

GCTGGGAAAGGAGACTTTGAGACGCTAGAAAAGAAGGTTCTAGAGTGGGGTGAGCCCACTGTTGCATCCGGCAAACAGgtaaatgtgt ... tcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGTCCATAGGTCCAGGAATAAGCAAGGGTGCGCCCTCCTCCGAACACGCACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

accattgcgctgatggttgcttattaggtatgtcatgatgtgctttcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGTCCATAGGTCCAGGAATAAGCAAGGGTGCGCCCTCCTCCGAACACGCACT
       cgctgat  putative branch site (score: 262)
                                        tgctttcct  putative PPT
                    ttatta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatgtgttgacagtctaggcgtcctctccaccattgcgctgatggttgcttattaggtatgtcatgatgtgctttcctgtgcagGAACTGGCGGAGATTCTGTTCCAGTCTGCCCTATAGATGATGGTGCCATGTCCATAGGTCCAGGAATAAGCAAGGGTGCGCCCTCCTCCGAACACGCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC