RetrogeneDB ID: retro_rnor_1415

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:5832936..5833530(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Ddx3x
• Ensembl ID: ENSRNOG00000023383
• Aliases: None
• Description: ATP-dependent RNA helicase DDX3X [Source:RefSeq peptide;Acc:NP_001101716]

Sequence

>retro_rnor_1415
GAAGGATATGTCTGCACCAGTATCCATGGAGACTGTTCTCCGAGAGATAGAGAAGCGGCCCTTCACCAGTTCCACTCAGG
AAAAAGACCAATTCTAGTGGTTACAGCAGTAGCAGCAAGAGGATTGGATATTTCAAATGTGAAACATGTTATTAATTTTG
ACCTGCCTAGTGATATCGAAGACTATGTGCATCGGCATAGACCATTCGGGGCATGTAGGAAACCTTGGTCTTGCCACCTC
ATTCTTTAATGAAAGGAATATAAATATCACTAAGGATTTACTGGATCTCCTTGTTGAAGCAAAACAGGAAGTGCCATCTT
GGTTAGAAAACATGGCTTTCGAACACCATAAGGGCAGCAGTTGTGGACCTTCTAAGAGTAGTAGTTTTAGTGGAGGATTT
GGTGCCAGAGGCCGTCGACAGAGTAGCTGTGTCAGCAGTTCCAGCTTCAGCAGCAGCCGTGCAAGCAGCAGTCAAAGAGG
TGGAGGTGGTCATGGCAGCAGCAGAGGATTTGGTAGAGGTGGCTACGGACGAGCTTTTTACAACAGTGATGGATATGGGG
AAATCCACTCCCAGGGGGTTACAGGTGGGGAAAC

Alignment

ORF - retro_rnor_1415 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.66 %
• Parental protein coverage: 63.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EGYACTSIHGDRSQRDREEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHR-IGRT
          EGY.CTSIHGD.S.RDRE.ALHQF.SGK.PILV.TAVAARGLDISNVKHVINFDLPSDIE.YVHR.I...
Retrocopy EGYVCTSIHGDCSPRDREAALHQFHSGKRPILVVTAVAARGLDISNVKHVINFDLPSDIEDYVHR>IDHS

Parental  GRVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAFEHHYKGSSRGRSKSSRFSGGFGARDY
          G.VGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAFEHH.KGSS.G.SKSS.FSGGFGAR..
Retrocopy GHVGNLGLATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAFEHH-KGSSCGPSKSSSFSGGFGARGR

Parental  RQSSGASSSSFSSSRASSSRSGGGGHGSSRGFGGGGYG-GFYNSDGYGGNYNSQGVDW-WGN
          RQSS..SSSSFSSSRASSS..GGGGHGSSRGFG.GGYG..FYNSDGY.G...SQGV...WGN
Retrocopy RQSSCVSSSSFSSSRASSSQRGGGGHGSSRGFGRGGYGRAFYNSDGY-GEIHSQGVTG<WGN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	196.35 RPM
SRP017611_kidney	0.00 RPM	362.10 RPM
SRP017611_liver	0.00 RPM	219.40 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1415 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1415 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1415 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035907	1 retrocopy	retro_btau_1846,
Callithrix jacchus	ENSCJAG00000009050	2 retrocopies	retro_cjac_1428, retro_cjac_4062,
Cavia porcellus	ENSCPOG00000013557	2 retrocopies	retro_cpor_326, retro_cpor_53,
Equus caballus	ENSECAG00000009901	1 retrocopy	retro_ecab_413,
Homo sapiens	ENSG00000215301	1 retrocopy	retro_hsap_4709,
Macaca mulatta	ENSMMUG00000017569	2 retrocopies	retro_mmul_1898, retro_mmul_2504,
Mus musculus	ENSMUSG00000000787	1 retrocopy	retro_mmus_205,
Ornithorhynchus anatinus	ENSOANG00000011274	1 retrocopy	retro_oana_64,
Pongo abelii	ENSPPYG00000020257	1 retrocopy	retro_pabe_3657,
Pan troglodytes	ENSPTRG00000022488	1 retrocopy	retro_ptro_3130,
Rattus norvegicus	ENSRNOG00000023383	1 retrocopy	retro_rnor_1415 ,