RetrogeneDB ID: retro_rnor_1351

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:42042886..42043411(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Dctn5
• Ensembl ID: ENSRNOG00000018048
• Aliases: Dctn5, RGD1305654
• Description: dynactin subunit 5 [Source:RefSeq peptide;Acc:NP_001032867]

Sequence

>retro_rnor_1351
ATGGAGTTGGGTGAACTGCTGTACAAGTCCGAGTACAGTGAGACGGCATCTGGGAACAATGTTAGTCGCCAGTCTGTTTT
GTGTAGAAGCCAGGACGTTGTTCTCAACGGCATGACCATTATAATGAATGACTGTATATACAAGGAGACCTGGTAAATGT
AGGAGTTGGATGTCACTGTGTTGTAAAAAACCATAGTGTCATAAGGCCATCATTCAAAAAATTCAGCAACGGTGTTGCAT
TCTTTTCTCTGCATATTGGGGATCATGCCTTTATTGAGGAAGATTGTGGGGTCAATGCTACCCAGATTGGCTCTTATGTT
TGTGTTGGGAAGGGCCATGTGATTGGGCGCTGGTGTGCCTTGAAAGACTGCTGCAACATTCTTGACAAATTATTACCTCC
AGAAACTGTGATTCCCTCCATTCACTGTCTTCTCCAGCTGTCCAGGACTTTTCTGAGGAAAGCTCCCAGAGCGTACACAG
GAACTGATGATCAATATCACCAAAAGCTACTGCCAGAAGTTTCTA

Alignment

ORF - retro_rnor_1351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.77 %
• Parental protein coverage: 97.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MELGELLYNKSEYIETASGNKVSRQSVLCGSQNIVLNGKTIIMNDCI-IRGDLANVRVGRHCVVKSRSVI
          MELGELLY.KSEY.ETASGN.VSRQSVLC.SQ..VLNG.TIIMNDCI.I.GDL.NV.VG.HCVVK..SVI
Retrocopy MELGELLY-KSEYSETASGNNVSRQSVLCRSQDVVLNGMTIIMNDCI<IQGDLVNVGVGCHCVVKNHSVI

Parental  RPPFKKFSKGVAFFPLHIGDHVFIEEDCVVNAAQIGSYVHVGKNCVIGRRCVLKDCCKILDNTVLPPETV
          RP.FKKFS.GVAFF.LHIGDH.FIEEDC.VNA.QIGSYV.VGK..VIGR.C.LKDCC.ILD...LPPETV
Retrocopy RPSFKKFSNGVAFFSLHIGDHAFIEEDCGVNATQIGSYVCVGKGHVIGRWCALKDCCNILDK-LLPPETV

Parental  V-PPFTVFSGCPGLFSGELPECTQELMIDVTKSYYQKFL
          ..PPFTVFS.CPGLF.G.LPE.TQELMI..TKSY.QKFL
Retrocopy I>PPFTVFSSCPGLF*GKLPERTQELMINITKSYCQKFL

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	42.85 RPM
SRP017611_kidney	0.00 RPM	32.03 RPM
SRP017611_liver	0.00 RPM	10.89 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1351 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1351 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1351 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	ENSBTAG00000006410	1 retrocopy	retro_btau_1203,
Callithrix jacchus	ENSCJAG00000020623	1 retrocopy	retro_cjac_1687,
Homo sapiens	ENSG00000166847	1 retrocopy	retro_hsap_260,
Gorilla gorilla	ENSGGOG00000012834	1 retrocopy	retro_ggor_309,
Microcebus murinus	ENSMICG00000007806	1 retrocopy	retro_mmur_1082,
Myotis lucifugus	ENSMLUG00000012148	1 retrocopy	retro_mluc_140,
Mus musculus	ENSMUSG00000030868	2 retrocopies	retro_mmus_2733, retro_mmus_625,
Nomascus leucogenys	ENSNLEG00000012015	1 retrocopy	retro_nleu_863,
Pongo abelii	ENSPPYG00000007194	2 retrocopies	retro_pabe_1729, retro_pabe_405,
Pan troglodytes	ENSPTRG00000007891	1 retrocopy	retro_ptro_220,
Rattus norvegicus	ENSRNOG00000018048	2 retrocopies	retro_rnor_1351 , retro_rnor_1847,