RetrogeneDB ID: retro_rnor_2571

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:59189524..59190236(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000022382
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Atp1b3
• Ensembl ID: ENSRNOG00000011501
• Aliases: Atp1b3, NKAB3S
• Description: Sodium/potassium-transporting ATPase subunit beta-3 [Source:UniProtKB/Swiss-Prot;Acc:Q63377]

Sequence

>retro_rnor_2571
TACCTAGTTTTTTATGGGTTCTTGGCTGCACTCTTCATATTCACCATGTGGGCCATGCTCCAGACTATGAATGACGAGGT
TTCGAAGTACCGAGACCAGATTCCTAGTCCAGGACTTATGGTTTTCCCCAAACCACCGACTGCCTTGGATTATACATACA
GCATGTCTGACCCACATACTTATAAAAAGTTTGTTGAAGACGTGAAGAATTTCCTAAAGCCATATTCTGTGGAAGAACAG
AAGAATCTCACAGATTGCCCTGGTGGGACACTTTTTCATCAGGAGGGTCCAGATTATAGTGCGTGTCAGTTTCCGGTTTC
CTTGCTTCAAGAATGTAGTGGTGTGAATGATTCTAATTTTGGCTACTCCAAAGGACAACCTTGTGTTCTTGTGAAGATGA
ACAGAATAATCGAGTTCGTCCCTGATGGAGCTCCATATATTACGTGTATTACAAAGGAAGAAAACATAGCAAATATAGTA
ACGTATCCTGATGATGGACTTATAGACTTAAAGTATTTTCCATATTATGGGAAAAAAACGGCACGTTGGATATCGACAGC
CCCTAGTTGCCGTCCAGGTCATATTTGGGACCGATGCTACCAAGAAAGAAGTAACAATTGAGTGCCAAATTGATGGAACC
AGGAACCTAAAAAACAAGAATGAATGTGACAAGTTCTTGGGACGAGTTTCATTTAAAGTCATAGCACATGCC

Alignment

ORF - retro_rnor_2571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.8 %
• Parental protein coverage: 84.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YLVFYGFLAALFTFTMWVMLQTLNDEVPKYRDQIPSPGLMVFPKPPTALDYTYSMSDPHTYKKFVEDLKN
          YLVFYGFLAALF.FTMW.MLQT.NDEV.KYRDQIPSPGLMVFPKPPTALDYTYSMSDPHTYKKFVED.KN
Retrocopy YLVFYGFLAALFIFTMWAMLQTMNDEVSKYRDQIPSPGLMVFPKPPTALDYTYSMSDPHTYKKFVEDVKN

Parental  FLKPYSVEEQKNLTDCPGGALFHQEGPDYSACQFPVSLLQECSGVNDSNFGYSKGQPCVLVKMNRIIELV
          FLKPYSVEEQKNLTDCPGG.LFHQEGPDYSACQFPVSLLQECSGVNDSNFGYSKGQPCVLVKMNRIIE.V
Retrocopy FLKPYSVEEQKNLTDCPGGTLFHQEGPDYSACQFPVSLLQECSGVNDSNFGYSKGQPCVLVKMNRIIEFV

Parental  PDGAPYITCITKEENIANIVTYPDDGLIDLKYFPYY-GKKRHVGYRQPLVAVQVIFGADATKKEVTIECQ
          PDGAPYITCITKEENIANIVTYPDDGLIDLKYFPYY.GKKRHVGYRQPLVAVQVIFG.DATKKEVTIECQ
Retrocopy PDGAPYITCITKEENIANIVTYPDDGLIDLKYFPYY>GKKRHVGYRQPLVAVQVIFGTDATKKEVTIECQ

Parental  IDGTRNLKNKNERDKFLGRVSFKVIAHA
          IDGTRNLKNKNE.DKFLGRVSFKVIAHA
Retrocopy IDGTRNLKNKNECDKFLGRVSFKVIAHA

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	0.07 RPM	62.77 RPM
SRP017611_kidney	0.28 RPM	81.16 RPM
SRP017611_liver	0.00 RPM	17.21 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2571 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2571 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2571 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014140	5 retrocopies	retro_btau_1136, retro_btau_1322, retro_btau_1743, retro_btau_318, retro_btau_920,
Choloepus hoffmanni	ENSCHOG00000007515	4 retrocopies	retro_chof_1000, retro_chof_1421, retro_chof_2393, retro_chof_2445,
Callithrix jacchus	ENSCJAG00000001981	1 retrocopy	retro_cjac_309,
Cavia porcellus	ENSCPOG00000003739	4 retrocopies	retro_cpor_1181, retro_cpor_1468, retro_cpor_1506, retro_cpor_222,
Equus caballus	ENSECAG00000019885	2 retrocopies	retro_ecab_1084, retro_ecab_468,
Homo sapiens	ENSG00000069849	2 retrocopies	retro_hsap_1387, retro_hsap_2263,
Loxodonta africana	ENSLAFG00000010553	1 retrocopy	retro_lafr_815,
Mus musculus	ENSMUSG00000032412	2 retrocopies	retro_mmus_2174, retro_mmus_3427,
Nomascus leucogenys	ENSNLEG00000004663	1 retrocopy	retro_nleu_1286,
Otolemur garnettii	ENSOGAG00000008662	1 retrocopy	retro_ogar_2284,
Procavia capensis	ENSPCAG00000013927	1 retrocopy	retro_pcap_350,
Pongo abelii	ENSPPYG00000014169	1 retrocopy	retro_pabe_1953,
Pan troglodytes	ENSPTRG00000015476	2 retrocopies	retro_ptro_1603, retro_ptro_951,
Rattus norvegicus	ENSRNOG00000011501	2 retrocopies	retro_rnor_2571 , retro_rnor_789,
Sus scrofa	ENSSSCG00000011676	3 retrocopies	retro_sscr_889, retro_sscr_945, retro_sscr_95,
Ictidomys tridecemlineatus	ENSSTOG00000013235	1 retrocopy	retro_itri_1663,
Tupaia belangeri	ENSTBEG00000001004	1 retrocopy	retro_tbel_3620,
Tarsius syrichta	ENSTSYG00000000222	1 retrocopy	retro_tsyr_330,
Tursiops truncatus	ENSTTRG00000012038	1 retrocopy	retro_ttru_333,