RetrogeneDB ID: retro_rnor_2019

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:232076873..232077225(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zfand6
• Ensembl ID: ENSRNOG00000013506
• Aliases: Zfand6, Za20d3, zgc:101121
• Description: AN1-type zinc finger protein 6 [Source:UniProtKB/Swiss-Prot;Acc:Q6DGF4]

Sequence

>retro_rnor_2019
ACATCGGAGGACAAAGCCGTATCTGAGACAGGAGACCTGCAAGGACCCAGAGCAGCAGAGGGCCTCGTTCCTCTCGAATG
TGATCCTCCATCTTCAGTGTCAGACACGACACAGCAGCCATGTGAGGAGCAAAGCAAGTCTCTTGCAAAACTAAGACAAA
ACAAGAATCGCTGTTTCATGTGCAGGAAGAAAGTGGGACTTTACCGGGTGTGAACGCCGGTGTGGACATGTTTACTGTGG
TGTGCACCGTTCCTCAGATGGTCACAATTGCTCTCACAATTACAAAGTTGATGTTGCTGAGAAAATCAGAAAAGAAAATA
CAGTAGTTGTCGGTGAAAAGATCCAGAAGCTT

Alignment

ORF - retro_rnor_2019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.9 %
• Parental protein coverage: 52.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TSVDKAVSETEDLQGPR-AEGLVPLECDPPSSVSDTTQQPSEEQSKSLEKPKQKKNRCFMCRKKVGL-TG
          TS.DKAVSET.DLQGPR.AEGLVPLECDPPSSVSDTTQQP.EEQSKSL.K..Q.KNRCFMCRKKVGL.TG
Retrocopy TSEDKAVSETGDLQGPRAAEGLVPLECDPPSSVSDTTQQPCEEQSKSLAKLRQNKNRCFMCRKKVGL>TG

Parental  FECRCGNVYCGVHRYSDVHNCSYNYKADAAEKIRKENPVVVGEKIQKI
          .E.RCG.VYCGVHR.SD.HNCS.NYK.D.AEKIRKEN.VVVGEKIQK.
Retrocopy CERRCGHVYCGVHRSSDGHNCSHNYKVDVAEKIRKENTVVVGEKIQKL

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	37.31 RPM
SRP017611_kidney	0.00 RPM	58.69 RPM
SRP017611_liver	0.00 RPM	43.10 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2019 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2019 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2019 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012321	1 retrocopy	retro_btau_593,
Choloepus hoffmanni	ENSCHOG00000009491	2 retrocopies	retro_chof_1516, retro_chof_2072,
Felis catus	ENSFCAG00000012931	2 retrocopies	retro_fcat_1024, retro_fcat_1998,
Homo sapiens	ENSG00000086666	1 retrocopy	retro_hsap_4153,
Gorilla gorilla	ENSGGOG00000015621	1 retrocopy	retro_ggor_2790,
Loxodonta africana	ENSLAFG00000006722	1 retrocopy	retro_lafr_587,
Monodelphis domestica	ENSMODG00000019428	1 retrocopy	retro_mdom_685,
Nomascus leucogenys	ENSNLEG00000008870	1 retrocopy	retro_nleu_1387,
Pan troglodytes	ENSPTRG00000007361	2 retrocopies	retro_ptro_1375, retro_ptro_2824,
Rattus norvegicus	ENSRNOG00000013506	1 retrocopy	retro_rnor_2019 ,
Sus scrofa	ENSSSCG00000001779	2 retrocopies	retro_sscr_1206, retro_sscr_1207,