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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgtaatattttgtgccagaaacatattttctcatctttctggttcctcttatttttttactatttgatgactgatcattgtttctaatgatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGGCTCAATTACTTTGATGAATTAGAAAAT

Basic information

species Zea mays
transcript GRMZM5G825854_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825854_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os08g34970.1 (Oryza sativa), 3'ss of exon 6
aatgtaatatt-ttgtgccagaaacatattttctcatctttctggttcctcttatttttttactatttgatgactgatcattgtttctaatgatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGGCTCAATTACTTTGATGAATTAGAAAAT
 || || | |  || ||||| |    |  |  ||| ||  | |  ||  |    | |||     | | ||  |    |  |   ||| |||| |  |||||||| | ||||||||||||||||| ||||||||||| ||||||||||| ||| | || |||||||||||||| ||||||
tatatattctcattttgccatattgctggtccctcttccgtttttttaatgaagtgtttcagtcaatggactatcatttctaaattcgaatg-taatgcagTTGTTGGAGAAACAAAGGCTGATTGAGTTTGCAGAAGCACTTCGAAGTAGGTTGAACTACTTTGATGAATTGGAAAAT

upper sequence: GRMZM5G825854_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g00350.t01 (Vitis vinifera), 3'ss of exon 7
aatgtaatattttgtgccagaaacatattttctcatctttctggttcctcttatttttttactat-ttgatgactgatcattgtttctaatgatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGGCTCAATTACTTTGATGAATTAGAAAAT
|    |||   ||  |        |  || ||| ||  |||| |    | | ||| |   || || |  ||  || |      ||| |  |     ||||| | || ||||||||||| ||||| ||||||||||| |||||||| ||||  ||||| |||||||| || || || |||
ataacaattagtttagtttagtttagtttatcttattcttcttgaagatat-attctcacacaatatcaatctcttacatggttttttgttcccattgcagCTAGTAGAGAAACAAAGACTGATTGAGTTTGCAGAAGCACTTCGCAGCAAACTCAACTACTTTGACGAGTTGGAGAAT
















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|93281267|gb|EB673531.1|EB673531
EST:     CAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTT                         TTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGG
genomic: CAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTTgtatgtctgt ... gatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGG
EST: gi|149104241|gb|EE289677.2|EE289677
EST:     CAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTT                         TTGGTTGAGAAACAAAGGCTGATCGAGTTTG
genomic: CAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTTgtatgtctgt ... gatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTG
EST: gi|211066409|gb|FL073783.1|FL073783
EST:     CAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTT                         TTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGG
genomic: CAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTTgtatgtctgt ... gatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGG
EST: gi|148952057|gb|EC897846.2|EC897846
EST:     CAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTT                         TTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGG
genomic: CAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTTgtatgtctgt ... gatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGG
EST: gi|91872014|gb|EB401971.1|EB401971
EST:     CAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTT                         TTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGG
genomic: CAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTTgtatgtctgt ... gatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGG
EST: gi|32859413|gb|CD999094.1|CD999094
EST:     CAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTT                         TTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGG
genomic: CAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTTgtatgtctgt ... gatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGG

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: 48 (upstream exon), 33 (downstream exon)
Score: 162

GTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTTgtatgtctgt ... gatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGGCTCAATTACTTTGATGAATTAGAAAAT


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 133

GTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTTgtatgtctgt ... gatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGGCTCAATTACTTTGATGAATTAGAAAAT


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 202

GTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTTgtatgtctgt ... gatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGGCTCAATTACTTTGATGAATTAGAAAAT


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 151

GTTGATGATACATTGAGCTTATTTGAAGAACTGCAGTCTTTGCACTCAAGCGTTGCCACGAAGACAAAAACTTTGCATGATGCTTGCGACCAACTTgtatgtctgt ... gatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGGCTCAATTACTTTGATGAATTAGAAAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctcttatttttttactatttgatgactgatcattgtttctaatgatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGGCTCAATTACTTTGATGAATTAGAAAAT
                                      ttctaat  putative branch site (score: 151)
     ttatttttttactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatgtaatattttgtgccagaaacatattttctcatctttctggttcctcttatttttttactatttgatgactgatcattgtttctaatgatggtgcagTTGGTTGAGAAACAAAGGCTGATCGAGTTTGCAGAGGCACTTCGAAGCAGGCTCAATTACTTTGATGAATTAGAAAAT

- - - - - - - - - - aaacata
- - - - - - - - - - - - - - - - - - ctttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttct