RetrogeneDB ID: retro_rnor_2386

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:106306330..106307075(-)
• Located in intron of: ENSRNOG00000009296

Retrocopy information

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

Parental gene information

• Parental gene symbol: Tmem183a
• Ensembl ID: ENSRNOG00000003594
• Aliases: Tmem183a, RGD1309892, Tmem183
• Description: Transmembrane protein 183 [Source:UniProtKB/Swiss-Prot;Acc:Q68FS7]

Sequence

>retro_rnor_2386
GATGGGGCTGGAGAAGAGGATCCTGTGGATATCTGGCTGCTGCTGGCTTCCTACATCCGTCCTGAGGACACTGTGAACTT
TTCCCTGATTTATAAGAATGCTTGGACTGTCACTTGCACTGCTGCCTTTTGGACCAGGTTGTACCAAAGGCACTACACGC
TGGGTGCTTCTCTACCTTTGCGGCTGCAACCAGAGTCCATGGAGAAGCTGTGCTGTCTCTGGGCATGTGTGATTCGATCT
CTGTACCATATGTAAGAACCGTTTGCTGCTCGAATCTCCAGGAACCTTGCCATTCCGGAAAGCACTCCCAGCACACTGAA
GAATTCCAAATGCTTACTTTTCTGGTGCAGAAAGATTGTTGGGATCAGACAAGAACCAGCATGGGAGTTCAACTTCAAGT
TCAAAAAACAGTCCCCTCGATGAAAGAGCGAGTGTACGGAACGGTTGCAATCGCCCATTCAGTATCAAGATGTTCATACC
AACCCTGACCAGGACTGCTGCCTGCTGCAGGTCACCTCCCTCAACTTCGTCTTTACTCCTTCCCATTGCCATGGGAATGA
TATTTACCTTGTTTACTATTAATGTGAGTTCAGACATGCGGCATCATCGAGTGAGACTGGTGTTCCAAGATTCTTCCGTC
TGTGGTGGTCAGCATCTGCACGGTGAACAGGATGTGCAAGCCGTCCTGGACCCAGTGAACAGTGTTCGGCTCTTTGACTG
GTGGCATCCGCAGTTCTCCCTGAGA

Alignment

ORF - retro_rnor_2386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.54 %
• Parental protein coverage: 66.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGAGGEEYPMDIWLLLASYIRPEDIVNFSLICKNAWTVTCTAAFWTRLYRRHYTLDASLPLRLRPESMEK
          DGAG.EE.P.DIWLLLASYIRPED.VNFSLI.KNAWTVTCTAAFWTRLY.RHYTL.ASLPLRL.PESMEK
Retrocopy DGAG-EEDPVDIWLLLASYIRPEDTVNFSLIYKNAWTVTCTAAFWTRLYQRHYTLGASLPLRLQPESMEK

Parental  LRCLRACVIRSLYHMYEPFAARISKNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWEFNFKFKKQSP
          L.CL.ACVIRSLYHM.EPFAARIS.N.AIPESTPSTLKNSKCLLFWCRKIVG.RQEP.WEFNFKFKKQSP
Retrocopy LCCLWACVIRSLYHM*EPFAARISRNLAIPESTPSTLKNSKCLLFWCRKIVGIRQEPAWEFNFKFKKQSP

Parental  RLKSKCMERLQPPIQYQDVHTNPDQD-C-CLLQVTTLNFIFIPIVMGMIFTLFTINVSTDMRHHRVRLVF
          R.KS.C.ERLQ.PIQYQDVHTNPDQD.C.C............PI.MGMIFTLFTINVS.DMRHHRVRLVF
Retrocopy R*KSECTERLQSPIQYQDVHTNPDQDCC>CCRSPPSTSSLLLPIAMGMIFTLFTINVSSDMRHHRVRLVF

Parental  QDSPVRGGQHLRSEQGVQVVLDPVHSVRLFDWWHPQYPFSLR
          QDS.V.GGQHL..EQ.VQ.VLDPV.SVRLFDWWHPQ..FSLR
Retrocopy QDSSVCGGQHLHGEQDVQAVLDPVNSVRLFDWWHPQ--FSLR

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	0.22 RPM	61.11 RPM
SRP017611_kidney	0.07 RPM	127.35 RPM
SRP017611_liver	0.07 RPM	52.92 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2386 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2386 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2386 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000008318	1 retrocopy	retro_etel_1835,
Felis catus	ENSFCAG00000013106	1 retrocopy	retro_fcat_3,
Homo sapiens	ENSG00000163444	3 retrocopies	retro_hsap_2808, retro_hsap_2863, retro_hsap_3157,
Gorilla gorilla	ENSGGOG00000009834	2 retrocopies	retro_ggor_1358, retro_ggor_2533,
Loxodonta africana	ENSLAFG00000018443	1 retrocopy	retro_lafr_149,
Macaca mulatta	ENSMMUG00000000801	1 retrocopy	retro_mmul_1532,
Nomascus leucogenys	ENSNLEG00000018106	2 retrocopies	retro_nleu_2541, retro_nleu_2663,
Otolemur garnettii	ENSOGAG00000000911	1 retrocopy	retro_ogar_3209,
Pongo abelii	ENSPPYG00000000340	2 retrocopies	retro_pabe_1333, retro_pabe_2627,
Pan troglodytes	ENSPTRG00000001864	2 retrocopies	retro_ptro_1902, retro_ptro_2278,
Rattus norvegicus	ENSRNOG00000003594	2 retrocopies	retro_rnor_1954, retro_rnor_2386 ,
Sus scrofa	ENSSSCG00000015473	1 retrocopy	retro_sscr_879,
Ictidomys tridecemlineatus	ENSSTOG00000012466	1 retrocopy	retro_itri_421,
Tarsius syrichta	ENSTSYG00000007009	1 retrocopy	retro_tsyr_717,