RetrogeneDB ID: retro_rnor_1454

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:40143161..40143947(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sec13
• Ensembl ID: ENSRNOG00000010628
• Aliases: Sec13, Sec13l1
• Description: None

Sequence

>retro_rnor_1454
ATGGTGTCAGTAATTAACACTGTGGATACCTCTCATGAGGACATGATTCATGATGCACAGATGGACTATTATGGCACCCG
CCTAGCAACCTGCTCCTCAGAAAGGTCTGTCAAAATTTTTGATGTGCGAAATGGAGGGCAGATCCTCATCGCAGACCTCG
GAGGTCATGAGGGGCCAGTGTGTCAGGTGGCCTGGGCTCACCCCATGTATGGCAATATCCTGTCTTCCTGTTCCTATGAC
CAGAAAGTCATTATCTGGAAGGAGGAAAACGGTACTTGGGGAAAGACCCATGAGCACTCAGGACATGACTCCTCAGTGAA
CTCTGTTTGCTGGGCCCCTCATGACTATGGCCTGATCCTGGCCTGTGGGAGTTCAGATGGTGCCATCTCGATGCTGACTT
ATACAGGGGAAGGCCAGTGGGAAGTGAAGAAGATTAACAATGCTCACACGATTGGCTGTAATAGTGTCAGTTGGGCTCCA
GCTGTTGTGCCTGGAAGCCTTATAGACCAACCATCGGGACAGAAACCCAATTAAATCAAGAAGTTTGCATCAGGTGGCTG
TGTCAACCTCATCAAGTTGTGGAGGGAAGAGGAGGATGGCCAGTGGAAGGAGGAGCAAAAGCTAGAGGCACACAGTGACT
GGGTTCTAGATGTTGCCTGGGGCCCCTCCATTGGCTTGCCCACCAGCACCATTGCCAGTTGCTCTCAGGATGGTCAAGTG
TTTATTTGGACTTGTGATGATGCCTCAGGCAATATGTGGTCACCTAAACTCCTACACAAGTTCAAT

Alignment

ORF - retro_rnor_1454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.04 %
• Parental protein coverage: 81.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSVINTVDTSHEDMIHDAQMDYYGTRLATCSSDRSVKIFDVRNGGQILIADLRGHEGPVWQVAWAHPMY
          MVSVINTVDTSHEDMIHDAQMDYYGTRLATCSS.RSVKIFDVRNGGQILIADL.GHEGPV.QVAWAHPMY
Retrocopy MVSVINTVDTSHEDMIHDAQMDYYGTRLATCSSERSVKIFDVRNGGQILIADLGGHEGPVCQVAWAHPMY

Parental  GNILASCSYDRKVIIWKEENGTWEKTHEHSGHDSSVNSVCWAPHDYGLILACGSSDGAISLLTYTGEGQW
          GNIL.SCSYD.KVIIWKEENGTW.KTHEHSGHDSSVNSVCWAPHDYGLILACGSSDGAIS.LTYTGEGQW
Retrocopy GNILSSCSYDQKVIIWKEENGTWGKTHEHSGHDSSVNSVCWAPHDYGLILACGSSDGAISMLTYTGEGQW

Parental  EVKKINNAHTIGCNAVSWAPAVVPGSLIDQPSGQKPNYIKKFASGGCDNLIKLWREEEDGQWKEEQKLEA
          EVKKINNAHTIGCN.VSWAPAVVPGSLIDQPSGQKPN.IKKFASGGC.NLIKLWREEEDGQWKEEQKLEA
Retrocopy EVKKINNAHTIGCNSVSWAPAVVPGSLIDQPSGQKPN*IKKFASGGCVNLIKLWREEEDGQWKEEQKLEA

Parental  HSDWVRDVAWAPSIGLPTSTIASCSQDGRVFIWTCDDASGNMWSPKLLHKFN
          HSDWV.DVAW.PSIGLPTSTIASCSQDG.VFIWTCDDASGNMWSPKLLHKFN
Retrocopy HSDWVLDVAWGPSIGLPTSTIASCSQDGQVFIWTCDDASGNMWSPKLLHKFN

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	20.56 RPM
SRP017611_kidney	0.00 RPM	52.62 RPM
SRP017611_liver	0.00 RPM	32.61 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1454 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1454 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1454 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005118	1 retrocopy	retro_cfam_278,
Callithrix jacchus	ENSCJAG00000016439	2 retrocopies	retro_cjac_1574, retro_cjac_908,
Felis catus	ENSFCAG00000011245	1 retrocopy	retro_fcat_541,
Homo sapiens	ENSG00000157020	1 retrocopy	retro_hsap_2630,
Microcebus murinus	ENSMICG00000002401	1 retrocopy	retro_mmur_1509,
Mus musculus	ENSMUSG00000030298	2 retrocopies	retro_mmus_2159, retro_mmus_3443,
Nomascus leucogenys	ENSNLEG00000004482	1 retrocopy	retro_nleu_642,
Otolemur garnettii	ENSOGAG00000017050	1 retrocopy	retro_ogar_1655,
Pongo abelii	ENSPPYG00000013658	1 retrocopy	retro_pabe_2333,
Pan troglodytes	ENSPTRG00000014619	1 retrocopy	retro_ptro_1774,
Rattus norvegicus	ENSRNOG00000010628	2 retrocopies	retro_rnor_1375, retro_rnor_1454 ,
Tursiops truncatus	ENSTTRG00000004395	1 retrocopy	retro_ttru_917,