RetrogeneDB ID: retro_rnor_973

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 13:85292136..85292358(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: 1110001A16Rik
• Ensembl ID: ENSRNOG00000040303
• Aliases: None
• Description: RIKEN cDNA 1110001A16 gene [Source:MGI Symbol;Acc:MGI:1915804]

Sequence

>retro_rnor_973
ATGACCCAAACCCTGAGACTCCTGGCTAAGAAGATCTTTAGAGGAGTTTTAGTAGCTGAACTTGTGGGCATTTTTACAGC
TTAATTTTTGTTTAAAAAGATGAACTTGAGCCAACATTTCAGGCAAAGGAGTGAGAAAATTCCCTTCATTTTGCAAGCTC
ATTACAAATCCATTGAACAGTATTGAATGTATGTAGAGACTGAAATCAAGAAAAATATTTGG

Alignment

ORF - retro_rnor_973 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 93.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTMEPLAKKIFKGVLAAELVGVFGAYFLFKKMNSSQDFRQTMSKTFPFILEVYYKSIEQSGMYGVREK
          M..T...LAKKIF.GVL.AELVG.F.A.FLFKKMN.SQ.FRQ..S...PFIL...YKSIEQ..MY...E.
Retrocopy MTQTLRLLAKKIFRGVLVAELVGIFTA*FLFKKMNLSQHFRQ-RSEKIPFILQAHYKSIEQY*MYVETEI

Parental  DQQKW
          ....W
Retrocopy KKNIW

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	2.52 RPM
SRP017611_kidney	0.00 RPM	2.30 RPM
SRP017611_liver	0.00 RPM	0.74 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_973 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_973 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_973 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017579	1 retrocopy	retro_amel_629,
Choloepus hoffmanni	ENSCHOG00000013008	2 retrocopies	retro_chof_328, retro_chof_49,
Felis catus	ENSFCAG00000023228	2 retrocopies	retro_fcat_1289, retro_fcat_1750,
Homo sapiens	ENSG00000218739	2 retrocopies	retro_hsap_2312, retro_hsap_4294,
Gorilla gorilla	ENSGGOG00000025368	2 retrocopies	retro_ggor_1755, retro_ggor_2869,
Mus musculus	ENSMUSG00000062691	2 retrocopies	retro_mmus_426, retro_mmus_509,
Pongo abelii	ENSPPYG00000029876	2 retrocopies	retro_pabe_2045, retro_pabe_3499,
Pan troglodytes	ENSPTRG00000033858	2 retrocopies	retro_ptro_1687, retro_ptro_2911,
Rattus norvegicus	ENSRNOG00000040303	2 retrocopies	retro_rnor_1144, retro_rnor_973 ,
Sus scrofa	ENSSSCG00000020689	2 retrocopies	retro_sscr_328, retro_sscr_434,
Tursiops truncatus	ENSTTRG00000006884	7 retrocopies	retro_ttru_1069, retro_ttru_1866, retro_ttru_1946, retro_ttru_274, retro_ttru_526, retro_ttru_57, retro_ttru_832,