RetrogeneDB ID: retro_rnor_501

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:175339326..175339688(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snx12
• Ensembl ID: ENSRNOG00000004036
• Aliases: Snx12, RGD1565585
• Description: sorting nexin 12 [Source:RefSeq peptide;Acc:NP_001102287]

Sequence

>retro_rnor_501
ATGTCAGACAGGGCAGTGGATGACACTCGGCGCCTTAACTTGAAGCCCCAGGACCTGACTGATGCTTACGGGGCCGCCTA
GTAACTTCCTGGAGATAGACATCTTTAATCCACAAGTGGGCGTGGGCTGCACGCGCTTTACCACCTATGAGGTTCGCAAG
TGGACAAACCTCCCCATCTTTAAGCTGAAAGAATCCTGTGTACGGCGACGCTATAGTGTCTTTGAGTGGCTGAAAATGAG
CTGGAGCGAGATAGTAAGATCGTAGTACCACACTGCCTGAGAAAGCCTTGAATTGGCAGCTCCCTTTCCGAGGAGATGAG
GAATCTTTCATTGAAGAAAGGAGGCAAGGTCTTGAACAGTTT

Alignment

ORF - retro_rnor_501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.5 %
• Parental protein coverage: 74.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSDTAVADTRRLNSKPQDLTDAYG-PPSNFLEIDIFNPQTVGVGRARFTTYEVRMRTNLPIFKLKESCVR
          MSD.AV.DTRRLN.KPQDLTDAYG.PPSNFLEIDIFNPQ.VGVG..RFTTYEVR..TNLPIFKLKESCVR
Retrocopy MSDRAVDDTRRLNLKPQDLTDAYG>PPSNFLEIDIFNPQ-VGVGCTRFTTYEVRKWTNLPIFKLKESCVR

Parental  RRYSDFEWLK-NELERDSKIVVP-PLPGKALKRQLPFRGDEGIFEESFIEERRQGLEQF
          RRYS.FEWLK.NELERDSKIVVP..LP.KAL..QLPFRGDE....ESFIEERRQGLEQF
Retrocopy RRYSVFEWLK<NELERDSKIVVP<TLPEKALNWQLPFRGDE----ESFIEERRQGLEQF

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	10.14 RPM
SRP017611_kidney	0.00 RPM	15.63 RPM
SRP017611_liver	0.00 RPM	0.74 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_501 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_501 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_501 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007871	1 retrocopy	retro_btau_1080,
Dasypus novemcinctus	ENSDNOG00000018281	1 retrocopy	retro_dnov_9,
Oryctolagus cuniculus	ENSOCUG00000014919	1 retrocopy	retro_ocun_1286,
Otolemur garnettii	ENSOGAG00000008973	1 retrocopy	retro_ogar_2565,
Rattus norvegicus	ENSRNOG00000004036	2 retrocopies	retro_rnor_1751, retro_rnor_501 ,
Sorex araneus	ENSSARG00000001830	1 retrocopy	retro_sara_452,