RetrogeneDB ID: retro_rnor_1043

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:38171003..38171538(-)
• Located in intron of: ENSRNOG00000002302

Retrocopy information

• Ensembl ID: ENSRNOG00000033977
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Anp32a
• Ensembl ID: ENSRNOG00000045651
• Aliases: None
• Description: acidic leucine-rich nuclear phosphoprotein 32 family member A [Source:RefSeq peptide;Acc:NP_037035]

Sequence

>retro_rnor_1043
ATGGAGAAACGGATTTTAGAGCTGCAGAACAGGACGCCCTCTGATGTGACCGAGCTGGTCCTGGATAACTGTCGGCCAAC
TGAAGGCAAAATCGAAGGCCTCGTGGATGAATCTGAAGACCTGGAATTCCTAAGTACAATCAACATAGGCCTCACCTCCG
TTTCGAACTTATCAACGTTAAACAAACTCAAGAAGCTTGAATTAAGCGAAAACAGAATCTCGGGGACCTGGAAGTATTGA
CAGAGAATCCGAACCTTAAGCGTCTAAATTTAAGTGGCAACAAAATAAAAGATCTCAGCACAATAGGGCCACAGAAGAAG
CTAGAGAATCTCAGGAGTCTATACTGTTTATGGGTGAGGTGACCAACCTGAATACCTACCGAGATGTGTTCAAGTTCCTG
CCCCAGGTCATGTACCTCGATGGCTATGTCAGGGACAAGGAGGCCCCTGACTCGGATGTTGAGGGTTACGTGGAGGATGA
CAATGAGGAAGATGAGGAGGAGGAAGAGTATGATGAGTATGCCCAGCTAGTGGAA

Alignment

ORF - retro_rnor_1043 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.16 %
• Parental protein coverage: 74.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDKRIYLELRNRTPSDVKELVLDNCRSIEGKIEGLTDEFEELEFLSTINVGLTSISNLPKLNKLKKLELS
          M.KRI.LEL.NRTPSDV.ELVLDNCR..EGKIEGL.DE.E.LEFLSTIN.GLTS.SNL..LNKLKKLELS
Retrocopy MEKRI-LELQNRTPSDVTELVLDNCRPTEGKIEGLVDESEDLEFLSTINIGLTSVSNLSTLNKLKKLELS

Parental  ENRISG-DLEVLAEKCPNLKHLNLSGNKIKDLSTIEPLKKLENLKSL-DLFNCEVTNLNAYRENVFKLLP
          ENRISG.DLEVL.E..PNLK.LNLSGNKIKDLSTI.P.KKLENL.SL..LF..EVTNLN.YR..VFK.LP
Retrocopy ENRISG<DLEVLTEN-PNLKRLNLSGNKIKDLSTIGPQKKLENLRSL<ILFMGEVTNLNTYRD-VFKFLP

Parental  QVMYLDGYDRDNKEAPDSDVEGYVEDDDEEDEDEEEYDEYAQLVE
          QVMYLDGY.RD.KEAPDSDVEGYVEDD.EEDE.EEEYDEYAQLVE
Retrocopy QVMYLDGYVRD-KEAPDSDVEGYVEDDNEEDEEEEEYDEYAQLVE

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	29.55 RPM
SRP017611_kidney	0.00 RPM	38.80 RPM
SRP017611_liver	0.00 RPM	16.14 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1043 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1043 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1043 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 16 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002339	2 retrocopies	retro_cjac_3305, retro_cjac_3799,
Dasypus novemcinctus	ENSDNOG00000015360	5 retrocopies	retro_dnov_1199, retro_dnov_1250, retro_dnov_1696, retro_dnov_836, retro_dnov_956,
Dipodomys ordii	ENSDORG00000008611	1 retrocopy	retro_dord_240,
Felis catus	ENSFCAG00000015773	1 retrocopy	retro_fcat_1188,
Homo sapiens	ENSG00000140350	3 retrocopies	retro_hsap_1479, retro_hsap_3117, retro_hsap_48,
Gorilla gorilla	ENSGGOG00000015417	1 retrocopy	retro_ggor_1134,
Loxodonta africana	ENSLAFG00000022560	1 retrocopy	retro_lafr_679,
Macaca mulatta	ENSMMUG00000022717	1 retrocopy	retro_mmul_1985,
Nomascus leucogenys	ENSNLEG00000013347	2 retrocopies	retro_nleu_15, retro_nleu_2383,
Otolemur garnettii	ENSOGAG00000003058	1 retrocopy	retro_ogar_2596,
Ochotona princeps	ENSOPRG00000015394	2 retrocopies	retro_opri_302, retro_opri_563,
Pongo abelii	ENSPPYG00000006595	2 retrocopies	retro_pabe_210, retro_pabe_2575,
Pan troglodytes	ENSPTRG00000007219	2 retrocopies	retro_ptro_2108, retro_ptro_758,
Rattus norvegicus	ENSRNOG00000045651	1 retrocopy	retro_rnor_1043 ,
Sarcophilus harrisii	ENSSHAG00000010906	1 retrocopy	retro_shar_540,
Tupaia belangeri	ENSTBEG00000016417	2 retrocopies	retro_tbel_4078, retro_tbel_4595,