RetrogeneDB ID: retro_rnor_1751

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 20:4666949..4667258(-)
• 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_1751
AACTTCCTGGAGATCGACGTGAGCAATCCCCAGACAGTGGGGGTCGGCCGGGGCCGCTTCACCACCTAAGAGATCAGGGT
CAAGACAAATCTTCCTATCTTCAAGCTGAAGGAATCCACTGTTAGAAGAAGATACAGTGACTTTGAATGGCTTCGAAGTG
AACTAGAGAGAGAGAGCTAGGTTGTCGTTCCCCCACTCCCGGGGAAAGCATTTTTGCGGCAGTTTCCTTTTAGAGGAGAC
GATGGAATATTTGATGATAATTTCATCAAGGAAAGGAAGCAAGGGCTGGAACAGTTCATAAACAAGATG

Alignment

ORF - retro_rnor_1751 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.67 %
• Parental protein coverage: 60.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NFLEIDIFNPQTVGVGRARFTTYEVRMRTNLPIFKLKESCVRRRYSDFEWLKNELERDSKIVVPPLPGKA
          NFLEID..NPQTVGVGR.RFTT.E.R..TNLPIFKLKES.VRRRYSDFEWL..ELER.S..VVPPLPGKA
Retrocopy NFLEIDVSNPQTVGVGRGRFTT*EIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERES*VVVPPLPGKA

Parental  LKRQLPFRGDEGIFEESFIEERRQGLEQFINKI
          ..RQ.PFRGD.GIF...FI.ER.QGLEQFINK.
Retrocopy FLRQFPFRGDDGIFDDNFIKERKQGLEQFINKM

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	8.48 RPM	10.14 RPM
SRP017611_kidney	11.17 RPM	15.63 RPM
SRP017611_liver	4.30 RPM	0.74 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1751 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1751 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1751 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,