RetrogeneDB ID: retro_rnor_789

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:30539500..30540105(+)
• Located in intron of: None

Retrocopy information

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

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_789
AGTCCAGGACTTACGGTTTTTCCAAAACCACTGACTGCCGCCTTGGAGTATACATACAGCGTGTCTGAGCCACATACTTA
TGAAGACCTGAAGAATTTCCTAGAGCCATATTCTGTGGGAGAACAGAAGAATCTTACACATTATCCTGATGGAGCACTTT
TTCATCAGCAAGTGTCTAGATTATAGTGTGTGTCAGTTTCCAGTTTCCTTGCTTCAAGATTGTAGTGGTGTGAATGATGC
TGACTTTGGCTATTCCAAGGGACAACCTTGTATTCTTGTGAAAATGAACAGAATAATTGAGCTAGTCCCAGACAGAGTTC
CACATATATATATAATGTGTGTGACAAAGGATGAAAACATAGCAAATATAGCAATGCATCCTGAATATGGACTTACAGAC
TTCAAGTATTTTCCATATTATGGGGGGAAATGGCACATTGGATATCGATAGCCCCTAGTTGACATCCAGGTCAAATTTGA
CTCTGGTGCTACCAAGAAAGAAATAGCAATTGAGTGCTAAATTGATGACTCCAAGAGCCTAAGAAACAAGAATGAACATG
ACAACTTTTGGGGACGAGTTTCGCTCAAAAGTCACAGCACATGCC

Alignment

ORF - retro_rnor_789 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.05 %
• Parental protein coverage: 72.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SPGLMVFPKPPTA-LDYTYSMSDPHTYKKFVEDLKNFLKPYSVEEQKNLTDCPGGALFHQEGP-DYSACQ
          SPGL.VFPKP.TA.L.YTYS.S.PHTY....EDLKNFL.PYSV.EQKNLT..P.GALFHQ....DYS.CQ
Retrocopy SPGLTVFPKPLTAALEYTYSVSEPHTY----EDLKNFLEPYSVGEQKNLTHYPDGALFHQQVS>DYSVCQ

Parental  FPVSLLQECSGVNDSNFGYSKGQPCVLVKMNRIIELVPDGAP--YITCITKEENIANIVTYPDDGLIDLK
          FPVSLLQ.CSGVND..FGYSKGQPC.LVKMNRIIELVPD..P..YI.C.TK.ENIANI...P..GL.D.K
Retrocopy FPVSLLQDCSGVNDADFGYSKGQPCILVKMNRIIELVPDRVPHIYIMCVTKDENIANIAMHPEYGLTDFK

Parental  YFPYYGKKRHVGYRQPLVAVQVIFGADATKKEVTIECQIDGTRNLKNKNERDKFLGRVSF-KVIAHA
          YFPYYG.K.H.GYR.PLV..QV.F...ATKKE..IEC.ID....L.NKNE.D.F.GRVS..KV.AHA
Retrocopy YFPYYGGKWHIGYR*PLVDIQVKFDSGATKKEIAIEC*IDDSKSLRNKNEHDNFWGRVSL>KVTAHA

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	62.77 RPM
SRP017611_kidney	0.00 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_789 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_789 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_789 has 0 orthologous retrocopies within eutheria group .

---

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,