RetrogeneDB ID: retro_rnor_2977

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:124155035..124155661(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Crls1
• Ensembl ID: ENSRNOG00000021273
• Aliases: None
• Description: Cardiolipin synthase [Source:UniProtKB/Swiss-Prot;Acc:Q5U2V5]

Sequence

>retro_rnor_2977
GCGCAGGTCCTCAGTGCCAGGCGCGTCAGGGCGCGCGCCACCAGCTCCTATGAAAATCCATGGACAATCCCACATTTGTT
GTCAATGATGAGAATTGGCCTGGCCACGGTGTTGGGCTATCTGATTCTTGAAGAAGATTTTAATGCTGCACTAGGTGTTT
TTGCTTTAGCCGGGCTAACGGATTTGTTGGATGGATTTATTGCTCGAAACCGGGCCAATCAGAAATCAGCTTTGGGAAGT
GCTCTTGATCCACTTGCTGATAAAGTTTTTATCAGCATCTTATATATTAGCTTGACCTATGCAGATCTTATTTCAGTCCC
ACTCACTTACATGATAATTTCAAGAGACGTATTGTTGATCGCTGTTGTGTTTTATGTCAGATACCGAACTCTGCCAGCAC
CGCGGACACTAGCTTAGTACATCAATCCTTGCTATACCCCTGCTAAGTTAAAACCAACATTCAGCAGCAAGGTCAATACA
GCAGTCCAGTTAATTTTGGTGGCAGCTTCTCTGGCAGCTGCAGTTTTCAATTATGCGGACAGCATTTATCTTCAGATACT
ATGGTGTTGTACAGCATTCCTACAACTGCATCAGCAGACAGTTAGTATCACTGTGGCCGGAAAACT

Alignment

ORF - retro_rnor_2977 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.14 %
• Parental protein coverage: 69.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AQAPSARWVRASATSSYENPWTIPNLLSMTRIGLAPVLGYLILEEDFNVALGVFALAGLTDLLDGFIARN
          AQ..SAR.VRA.ATSSYENPWTIP.LLSM.RIGLA.VLGYLILEEDFN.ALGVFALAGLTDLLDGFIARN
Retrocopy AQVLSARRVRARATSSYENPWTIPHLLSMMRIGLATVLGYLILEEDFNAALGVFALAGLTDLLDGFIARN

Parental  WANQKSALGSALDPLADKVLISILYISLTYADLIPVPLTYMIISRDVMLIAAVFYVRYRTLPTPRTLAKY
          .ANQKSALGSALDPLADKV.ISILYISLTYADLI.VPLTYMIISRDV.LIA.VFYVRYRTLP.PRTLA.Y
Retrocopy RANQKSALGSALDPLADKVFISILYISLTYADLISVPLTYMIISRDVLLIAVVFYVRYRTLPAPRTLA*Y

Parental  FNPCYATARLKPTFISKVNTAVQLILVAASLAAPVFNYADSIYLQILWCCTAF-TTAASAYSYYHYGRKT
          .NPCY..A.LKPTF.SKVNTAVQLILVAASLAA.VFNYADSIYLQILWCCTAF..T.ASA.S.YH.GRKT
Retrocopy INPCYTPAKLKPTFSSKVNTAVQLILVAASLAAAVFNYADSIYLQILWCCTAF<PTTASADS*YHCGRKT

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	9.35 RPM
SRP017611_kidney	0.00 RPM	30.70 RPM
SRP017611_liver	0.00 RPM	17.08 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2977 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2977 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2977 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010596	1 retrocopy	retro_amel_1758,
Bos taurus	ENSBTAG00000000065	1 retrocopy	retro_btau_1167,
Canis familiaris	ENSCAFG00000005934	1 retrocopy	retro_cfam_1002,
Equus caballus	ENSECAG00000023869	2 retrocopies	retro_ecab_247, retro_ecab_930,
Felis catus	ENSFCAG00000023647	1 retrocopy	retro_fcat_1393,
Microcebus murinus	ENSMICG00000011666	1 retrocopy	retro_mmur_751,
Mustela putorius furo	ENSMPUG00000006349	1 retrocopy	retro_mputfur_1021,
Rattus norvegicus	ENSRNOG00000021273	3 retrocopies	retro_rnor_2865, retro_rnor_2866, retro_rnor_2977 ,