RetrogeneDB ID: retro_rnor_422

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:19563559..19563845(+)
• Located in intron of: ENSRNOG00000015605

Retrocopy information

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

Parental gene information

• Parental gene symbol: Slmo2
• Ensembl ID: ENSRNOG00000046644
• Aliases: None
• Description: protein slowmo homolog 2 [Source:RefSeq peptide;Acc:NP_001009543]

Sequence

>retro_rnor_422
ATTTCATTTACAAATATGGTTTCAATAGAGGATAGGGTTTCATGACTTTCCTACAAACCTCAGGACCCAGGAAAGCCTGT
TGTGAATGAGGAAGCCATCATCACTACAAACCGGGGACAGCCTCAAGAGCTACCTTGAAGGACTCATGGCTCGCACTGTA
CCTTCAAAAGATAACAAAGGCTTTGAAGCAATGGGATGGGTGGTCCATTGGCTGAGGTTGAAGAATTCTGTATCGACAAG
AGGAAGCCTTAGGACACTCACGGCAGCTTTGGAAGAGCTGATGAAT

Alignment

ORF - retro_rnor_422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.47 %
• Parental protein coverage: 98.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ISFTNMVSVDER---LTYKPHPQDPEKTVLTQEALITVK-GVSLSSYLEGLMASTISSNANKGREAMEWV
          ISFTNMVS...R...L.YKP..QDP.K.V...EA.IT...G.SL.SYLEGLMA.T..S..NKG.EAM.WV
Retrocopy ISFTNMVSIEDRVS*LSYKP--QDPGKPVVNEEAIITTN>GDSLKSYLEGLMARTVPSKDNKGFEAMGWV

Parental  IHKLNAEIEELAASARGSIRTPMAAAAALVD
          .H.L.........S.RGS.RT..AA...L..
Retrocopy VHWLRL---KNSVSTRGSLRTLTAALEELMN

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	12.80 RPM
SRP017611_kidney	0.00 RPM	26.66 RPM
SRP017611_liver	0.00 RPM	9.35 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_422 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_422 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_422 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018905	4 retrocopies	retro_cjac_1286, retro_cjac_2921, retro_cjac_3171, retro_cjac_3236,
Dasypus novemcinctus	ENSDNOG00000014548	3 retrocopies	retro_dnov_1402, retro_dnov_2032, retro_dnov_2311,
Echinops telfairi	ENSETEG00000009651	3 retrocopies	retro_etel_1130, retro_etel_1262, retro_etel_632,
Loxodonta africana	ENSLAFG00000000300	1 retrocopy	retro_lafr_700,
Myotis lucifugus	ENSMLUG00000014907	2 retrocopies	retro_mluc_1887, retro_mluc_845,
Macaca mulatta	ENSMMUG00000007560	4 retrocopies	retro_mmul_1155, retro_mmul_1644, retro_mmul_2123, retro_mmul_539,
Monodelphis domestica	ENSMODG00000016608	5 retrocopies	retro_mdom_1596, retro_mdom_1619, retro_mdom_1620, retro_mdom_1655, retro_mdom_405,
Mus musculus	ENSMUSG00000016257	2 retrocopies	retro_mmus_2725, retro_mmus_630,
Oryctolagus cuniculus	ENSOCUG00000005621	8 retrocopies	retro_ocun_1944, retro_ocun_1954, retro_ocun_455, retro_ocun_486, retro_ocun_549, retro_ocun_619, retro_ocun_775, retro_ocun_926,
Ochotona princeps	ENSOPRG00000002550	8 retrocopies	retro_opri_1069, retro_opri_1090, retro_opri_141, retro_opri_216, retro_opri_45, retro_opri_663, retro_opri_683, retro_opri_770,
Rattus norvegicus	ENSRNOG00000046644	2 retrocopies	retro_rnor_422 , retro_rnor_423,
Sorex araneus	ENSSARG00000004671	2 retrocopies	retro_sara_282, retro_sara_430,