RetrogeneDB ID: retro_rnor_2942

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:75335132..75336066(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000021998
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Slc25a38
• Ensembl ID: ENSRNOG00000018552
• Aliases: Slc25a38, RGD1311914
• Description: solute carrier family 25 member 38 [Source:RefSeq peptide;Acc:NP_001025203]

Sequence

>retro_rnor_2942
GGGTTCGCGTCTCCCTTGATCAAGAAGGCGAGCACAGCGCTGCTACCATCGCAGGATGTAGAGAACACAGTGGAGACGCT
CATGTTACATCCAGTGATTAAGGCTTTCCTCTGCGGCTCCATCAGCGGAACCTTTTCCACGCTCCTCTTCCAGCCTCTGG
ACCTCCTCAAAACCCGCCTGCAGACCCTGCAGCCCTCAGATATAGGGCCCAGGGGTGTTGGGATGTTGGCTGTGTTCTTG
AAGGTGGTTGTCACAGAAAGTCTTCTGGGCCTTTGGAAAGGGATGTCTCCTTCCATTGTGAGATGTGTCCCTGGCGTTGG
AATCTCCTTTGGCACCCTGTATTCTTCCAAGCAGTATTTCTTGCGAGGCCATCCTCCCACTGCCATGGAGTCTGTCATCC
TGGGCATGGGCTCTCGCTCTATGGCAGAAGTCTGCATGTCACCCATCACAGTGGTCAAGACACGCTACGAGAGTGGGGCT
TACAGCTACCAGAGCGTCTGTGCAGCCCTGCGGAGCATCTGCTGTAGCGAGGGCCGCCGTGGCCTCTTCGGAGGCCTGAC
AGCAACTCTGCTTCGTGATGCCCCCTTCTCGGCGCTCTACCTGATGTTTTACAGCCAGACCAGGGCCACAGTGCTCCATG
GTACAGGCCAGCTGGATGCTGCTCTGATGCCCCTTGTTAATTTCAGCAGTGGGATATTTGCTTGCATTCTGGATTCACTG
GTGACTCAACCTGCAGACGTGATCAAAACCCATATGCAGCGCTCCCCAGTGAAAGTGTCAGTGCACTGGCCAAGTGGCCA
CCCTCATTCTCAAGCCCCATGGGCTGCGTGGCTTCTTTCATGGCAGCGTTCCCCGGGCCCTCCGTAAAACTCTGATGGCT
GCCATGGCATGGACTGTCTATGAAGAGATGGTGGCCAGGATGGGGCTCAAGTCC

Alignment

ORF - retro_rnor_2942 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.46 %
• Parental protein coverage: 95.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLASPVIEKARSALLPSQDVEDTVETLMLHPVIKAFLCGSISGTCSTLLFQPLDLLKTRLQTLQPSDVGP
          G.ASP.I.KA..ALLPSQDVE.TVETLMLHPVIKAFLCGSISGT.STLLFQPLDLLKTRLQTLQPSD.GP
Retrocopy GFASPLIKKASTALLPSQDVENTVETLMLHPVIKAFLCGSISGTFSTLLFQPLDLLKTRLQTLQPSDIGP

Parental  RRVGMLSVFLKVVRTESLLGLWKGMSPSIVRCVPGVGIYFGTLYSSKQYFLRGHPPTALESVILGMGSRS
          R.VGML.VFLKVV.TESLLGLWKGMSPSIVRCVPGVGI.FGTLYSSKQYFLRGHPPTA.ESVILGMGSRS
Retrocopy RGVGMLAVFLKVVVTESLLGLWKGMSPSIVRCVPGVGISFGTLYSSKQYFLRGHPPTAMESVILGMGSRS

Parental  VAGVCMSPITVVKTRYESGAYSYESVYAALRSIYCSEGSRGLFRGLTATLLRDAPFSGLYLMFYSQTRAT
          .A.VCMSPITVVKTRYESGAYSY.SV.AALRSI.CSEG.RGLF.GLTATLLRDAPFS.LYLMFYSQTRAT
Retrocopy MAEVCMSPITVVKTRYESGAYSYQSVCAALRSICCSEGRRGLFGGLTATLLRDAPFSALYLMFYSQTRAT

Parental  VLHGADELDAALMPLVNFSCGVFAGILASLVTQPADVIKTHMQLSTV-KCQCIGQVATLILKTHGLRGFF
          VLHG...LDAALMPLVNFS.G.FA.IL.SLVTQPADVIKTHMQ.S.V.KCQC.GQVATLILK.HGLRGFF
Retrocopy VLHGTGQLDAALMPLVNFSSGIFACILDSLVTQPADVIKTHMQRSPV>KCQCTGQVATLILKPHGLRGFF

Parental  HGSVPRALRRTLMAAMAWTVYEEMMAKMGLKS
          HGSVPRALR.TLMAAMAWTVYEEM.A.MGLKS
Retrocopy HGSVPRALRKTLMAAMAWTVYEEMVARMGLKS

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	15.75 RPM
SRP017611_kidney	0.07 RPM	37.75 RPM
SRP017611_liver	0.00 RPM	23.26 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2942 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2942 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2942 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000144659	1 retrocopy	retro_hsap_266,
Gorilla gorilla	ENSGGOG00000013530	1 retrocopy	retro_ggor_315,
Nomascus leucogenys	ENSNLEG00000005614	1 retrocopy	retro_nleu_868,
Pan troglodytes	ENSPTRG00000014772	1 retrocopy	retro_ptro_223,
Rattus norvegicus	ENSRNOG00000018552	1 retrocopy	retro_rnor_2942 ,
Tupaia belangeri	ENSTBEG00000015842	1 retrocopy	retro_tbel_1400,