RetrogeneDB ID: retro_rnor_1892

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:78881425..78881979(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Slc25a39
• Ensembl ID: ENSRNOG00000020994
• Aliases: Slc25a39, RGD1306193
• Description: Solute carrier family 25 member 39 [Source:UniProtKB/Swiss-Prot;Acc:Q4V8K4]

Sequence

>retro_rnor_1892
CTTCAGTCTCAGAGACCCTCAGTAGCCAGCAACTTGACAGCTCCCTCCAGATTCTGAAGTCTCTCCTACACCAAATCACC
CTCCCCTCCACAATCCCCAGGGAAGTGCCTCCTATACTACACTGGTGTCCTGGAGCCCCTGGACCTGTGCCCAAATGGTA
CTCGCTGCGCCACCTGGTATCAGGATCCTACACGGTTCACTGTCACCTTGGATGCCTTCGTGAAGGTTGTGAGGCATGAG
GGCATCAGGACCCTGTGGAGCGGCCTCCTAGCCACCCTGGTGATGACTGTGCCAGTTACTGCCATCTACTTCACTGCTTA
TGACCAACTCAAGGCCTTCCTATGTGGTCGTCCTTGACCTCTGACCTCTATGCACCCACAGTGGCTGGTGCACTCACCCG
AATGGGCAATGTGACAGTTGTCAGCCCCTTGGAGTTTATAAGGACCAAGCTGCAGGCTCAGCATGTGTCATACTTCGAAC
TGTCTACCTGTGTTCAAGCTGCGGTGGCTCAGGGTGGCTGGCGCTCACTGTGTCTGGCCTGGGGTCTCACAGCC

Alignment

ORF - retro_rnor_1892 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.95 %
• Parental protein coverage: 51.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQSQRPTVASELTTPSRFWSLSYTKSPSTLQSPGKCLLYCNGVLEPLYLCPNGTRCATWFQDPTRFTGTL
          LQSQRP.VAS.LT.PSRF.SLSYTKSPS..QSPGKCLLY..GVLEPL.LCPNGTRCATW.QDPTRFT.TL
Retrocopy LQSQRPSVASNLTAPSRF*SLSYTKSPSPPQSPGKCLLYYTGVLEPLDLCPNGTRCATWYQDPTRFTVTL

Parental  DAFVKIVRHEGTRTLWSGLPATLVMTVPATAIYFTAYDQLKAFLCGQ-SLTSDLYAPMVAGALARMGTVT
          DAFVK.VRHEG.RTLWSGL.ATLVMTVP.TAIYFTAYDQLKAFLCG..SLTSDLYAP.VAGAL.RMG.VT
Retrocopy DAFVKVVRHEGIRTLWSGLLATLVMTVPVTAIYFTAYDQLKAFLCGR<SLTSDLYAPTVAGALTRMGNVT

Parental  VVSPLELVRTKLQAQHVSYRELAACVQAAVAQGGWRSLWLGWGPTA
          VVSPLE..RTKLQAQHVSY.EL..CVQAAVAQGGWRSL.L.WG.TA
Retrocopy VVSPLEFIRTKLQAQHVSYFELSTCVQAAVAQGGWRSLCLAWGLTA

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	29.33 RPM
SRP017611_kidney	0.00 RPM	250.31 RPM
SRP017611_liver	0.00 RPM	116.86 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1892 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1892 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1892 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008556	1 retrocopy	retro_dnov_1866,
Echinops telfairi	ENSETEG00000002713	1 retrocopy	retro_etel_823,
Homo sapiens	ENSG00000013306	1 retrocopy	retro_hsap_290,
Myotis lucifugus	ENSMLUG00000001925	2 retrocopies	retro_mluc_2296, retro_mluc_646,
Monodelphis domestica	ENSMODG00000011561	1 retrocopy	retro_mdom_1102,
Pongo abelii	ENSPPYG00000008333	1 retrocopy	retro_pabe_383,
Pan troglodytes	ENSPTRG00000009272	1 retrocopy	retro_ptro_239,
Rattus norvegicus	ENSRNOG00000020994	2 retrocopies	retro_rnor_1892 , retro_rnor_2884,
Ictidomys tridecemlineatus	ENSSTOG00000004189	1 retrocopy	retro_itri_447,