RetrogeneDB ID: retro_rnor_1104

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:40505021..40505364(+)
• Located in intron of: ENSRNOG00000008059

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tm2d1
• Ensembl ID: ENSRNOG00000007527
• Aliases: Tm2d1, Bbp
• Description: TM2 domain-containing protein 1 precursor [Source:RefSeq peptide;Acc:NP_001102140]

Sequence

>retro_rnor_1104
TATAAACTACACAGCTCATGTTCAGTGTCTTCCAGCACCCAACACAACGTGTAAGGATTTGAAGCTCATTTTACTGGAAA
TGAGGTTGGTCTTCTCAAGCCCACATCTTGCCGAAATGTGAATGGCTATTCATACAAAGTGCCCGTTGCATTATCTCTTT
TTGGGGGATGGCTGGGAGCAGGTCAATTTTACCTTGGATATCCTGCCTTAGGCATGTTCAAGTTTTGCACCATAGGATTT
TGCAGAACTGGAAGCCTAATTGATTTCGTTCTTATTTCAATGCAGATTGTTGGACCTTAACATTGGAGGTAGTTACATTA
TAGACTGTTATGGAACCAGACTT

Alignment

ORF - retro_rnor_1104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.69 %
• Parental protein coverage: 55.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YTAHVQCFPAPNITCKDLSGNETHFTGSEVGFLKPISCRNVNGYSYKVAVALSLFLGWLGADRFYLGYPA
          Y..H..C......T.....G.E.HFTG.EVG.LKP.SCRNVNGYSYKV.VALSLF.GWLGA..FYLGYPA
Retrocopy YKLHSSCSVSSS-TQHNV*GFEAHFTGNEVGLLKPTSCRNVNGYSYKVPVALSLFGGWLGAGQFYLGYPA

Parental  LGLLKFCTVGFCGIGSLIDFVLISMQIVGP-SDGSSYIIDYYGTRL
          LG..KFCT.GFC..GSLIDFVLISMQIVGP...G.SYIID.YGTRL
Retrocopy LGMFKFCTIGFCRTGSLIDFVLISMQIVGP>NIGGSYIIDCYGTRL

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	20.20 RPM
SRP017611_kidney	0.00 RPM	27.56 RPM
SRP017611_liver	0.00 RPM	8.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1104 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1104 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1104 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011705	1 retrocopy	retro_amel_1290,
Canis familiaris	ENSCAFG00000018838	1 retrocopy	retro_cfam_1213,
Choloepus hoffmanni	ENSCHOG00000013535	1 retrocopy	retro_chof_1494,
Cavia porcellus	ENSCPOG00000012287	1 retrocopy	retro_cpor_471,
Equus caballus	ENSECAG00000015035	1 retrocopy	retro_ecab_556,
Erinaceus europaeus	ENSEEUG00000001567	1 retrocopy	retro_eeur_708,
Loxodonta africana	ENSLAFG00000013979	1 retrocopy	retro_lafr_662,
Mus musculus	ENSMUSG00000028563	2 retrocopies	retro_mmus_1412, retro_mmus_1981,
Rattus norvegicus	ENSRNOG00000007527	1 retrocopy	retro_rnor_1104 ,
Tupaia belangeri	ENSTBEG00000002089	3 retrocopies	retro_tbel_1156, retro_tbel_1730, retro_tbel_201,