RetrogeneDB ID: retro_rnor_1954

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:20789358..20790071(+)
• Located in intron of: None

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_1954
CCCAAACAGCTAGGCGATTCTTGTCTGGAAACTGCCAGCATATCCAAGAGAGGAAAGCGACTCAAGTTCTGGGCCCATCT
CGCCTGCTCGGGCTGAGTGACTGTGGCAGACTATGCCAACTCGGATCCAGTGGTGTGAGATCTGGACTGGTCAAGAAAGC
CGTGGCCAACTCTGTTCAACAGGAAGCAAAGTCACTGTTGTAGTTTGGAAGCATCCCAGGCTCCTCCTACTGAGGAGGCT
CTTTCTGGGGTGGGTGAACCATGTGACATCATGGACAGCAGTGATGAGATGGATGCCCAGGAGGAAAACTCTCAGGAAAG
ATCCGACTCCAAAAACAAGAAAAGCAAGGGACACAAAGCAAAGTCCCTGGATGGGGCTGTCAGGGAAGAGTATCCAATTG
ATGTTTGCCTGCTGCTGGCTTCTTATATCCGTCCTGAGGCCATCGTGAATTTTTCCCTGATTTATAGGAATGCTTGGACC
TGAACTTGCACTGTGCCTTTTGAACCAGGTTGTACCAAAAGCACGACACGTTAGATGCTTCTCTACCTTTGCAGCTGTGA
CCAGAGTCCGTGTAGAAGCTGTGCTGTCTCCAGGCATGTGTGATCTCATCTCTGTATCATATGTATGAACCGTTTGCTGC
TCCAATCTCCAAGATTCCAGTCATTCTTGAAAGCACTCCCAGCACACTGAAAAATTCCAAATGCTTACTTTGG

Alignment

ORF - retro_rnor_1954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.27 %
• Parental protein coverage: 62.77 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PGQLSGPRPDTVTMPKRGKRLKFRAHDACSGRVTVADYANSDPAV-VRSGRVKKAVANAVQQEVKSL-CG
          P.QL......T....KRGKRLKF.AH.ACSG.VTVADYANSDP.V.VRSG.VKKAVAN.VQQE.KSL.C.
Retrocopy PKQLGDSCLETASISKRGKRLKFWAHLACSG*VTVADYANSDPVV<VRSGLVKKAVANSVQQEAKSL>CS

Parental  LEASQVP-AEEALSGVGEPSDILDSSDEMDAQEESTQERSVSRKKKSKRHK-EDLDGAGGEEYPMDIWLL
          LEASQ.P..EEALSGVGEP.DI.DSSDEMDAQEE..QERS.S..KKSK.HK...LDGA..EEYP.D..LL
Retrocopy LEASQAPPTEEALSGVGEPCDIMDSSDEMDAQEENSQERSDSKNKKSKGHKAKSLDGAVREEYPIDVCLL

Parental  LASYIRPEDIVNFSLICKNAWTVTCTA-AFWTRLYRRHYTLDASLPLRLRPESMEKLRCLRACVIRSLYH
          LASYIRPE.IVNFSLI..NAWT.TCT..AF.TRLY..H.TLDASLPL.L.PES..KL.CL.ACVI.SLYH
Retrocopy LASYIRPEAIVNFSLIYRNAWT*TCTV<AF*TRLYQKHDTLDASLPLQL*PESV*KLCCLQACVISSLYH

Parental  MYEPFAARISKNPAIPESTPSTLKNSKCLLF
          MYEPFAA.ISK.P.I.ESTPSTLKNSKCLL.
Retrocopy MYEPFAAPISKIPVILESTPSTLKNSKCLLW

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	61.11 RPM
SRP017611_kidney	0.00 RPM	127.35 RPM
SRP017611_liver	0.00 RPM	52.92 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1954 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1954 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1954 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,