RetrogeneDB ID: retro_rnor_1966

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:47367632..47367946(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nme2
• Ensembl ID: ENSRNOG00000002671
• Aliases: Nme2, NDKB, nm23-2, p18-12d
• Description: Nucleoside diphosphate kinase B [Source:UniProtKB/Swiss-Prot;Acc:P19804]

Sequence

>retro_rnor_1966
CAAAACCTGAAGCAGCACTACATTCTCCTGAAAAACCATCCTTTCCTCCAGGGGCTAAAGTACATGAACTCAGGTCAAGG
CTCTTGGTGGCCATGGTTGGAAAGGGCTCAATCTAGTGAAAACAAGACGAGCAGATGCTGGGAGACACCAAACGAGCTGA
ATCTAAACCAGGCACCATTTGTGGGGATTTTTGCATTCAAGTTGTCAGGAACCTCTTTCGTGGTGGTGATGCAGTGGAGA
AAACTGAGGAAGAGATTGGTCTATGGTTTAAGCCCGGAGAACTGATTGATTCTAAGTCTTGTGCCCATGAATGG

Alignment

ORF - retro_rnor_1966 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.89 %
• Parental protein coverage: 68.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EHLKQHYIDLKDRPFF-PGL-VKYMNSGPVVAMV-WEGLNVVKTGRV-MLGETNPADSKPGTIRGDFCIQ
          ..LKQHYI.LK..PF..PG..V....S...VAMV.W.GLN.VKT.R..MLG.T..A.SKPGTI.GDFCIQ
Retrocopy QNLKQHYILLKNHPFL<PGAKVHELRSRLLVAMV<WKGLNLVKTRRA>MLGDTKRAESKPGTICGDFCIQ

Parental  VGRNIIHGSDSVESAEKEIGLWFKPEELIDYKSCAHDW
          V.RN...G.D.VE..E.EIGLWFKP.ELID.KSCAH.W
Retrocopy VVRNLFRGGDAVEKTEEEIGLWFKPGELIDSKSCAHEW

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	76.86 RPM
SRP017611_kidney	0.00 RPM	163.92 RPM
SRP017611_liver	0.00 RPM	72.08 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1966 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1966 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1966 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Bos taurus	ENSBTAG00000047186	1 retrocopy	retro_btau_1329,
Callithrix jacchus	ENSCJAG00000018395	5 retrocopies	retro_cjac_1765, retro_cjac_2517, retro_cjac_2642, retro_cjac_3940, retro_cjac_471,
Equus caballus	ENSECAG00000021658	1 retrocopy	retro_ecab_404,
Erinaceus europaeus	ENSEEUG00000003783	2 retrocopies	retro_eeur_156, retro_eeur_5,
Felis catus	ENSFCAG00000006742	5 retrocopies	retro_fcat_1083, retro_fcat_1117, retro_fcat_1475, retro_fcat_216, retro_fcat_663,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Loxodonta africana	ENSLAFG00000007784	1 retrocopy	retro_lafr_636,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Macaca mulatta	ENSMMUG00000001940	1 retrocopy	retro_mmul_1827,
Monodelphis domestica	ENSMODG00000012580	1 retrocopy	retro_mdom_1811,
Mustela putorius furo	ENSMPUG00000015573	4 retrocopies	retro_mputfur_1236, retro_mputfur_1590, retro_mputfur_327, retro_mputfur_912,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Oryctolagus cuniculus	ENSOCUG00000024946	1 retrocopy	retro_ocun_418,
Otolemur garnettii	ENSOGAG00000025331	9 retrocopies	retro_ogar_1326, retro_ogar_1875, retro_ogar_1997, retro_ogar_2373, retro_ogar_2393, retro_ogar_2779, retro_ogar_3299, retro_ogar_483, retro_ogar_95,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966 , retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Rattus norvegicus	ENSRNOG00000002693	3 retrocopies	retro_rnor_1198, retro_rnor_1600, retro_rnor_704,
Rattus norvegicus	ENSRNOG00000049152	1 retrocopy	retro_rnor_2679,
Sarcophilus harrisii	ENSSHAG00000014470	3 retrocopies	retro_shar_130, retro_shar_554, retro_shar_781,
Sus scrofa	ENSSSCG00000017591	1 retrocopy	retro_sscr_854,
Tupaia belangeri	ENSTBEG00000013053	6 retrocopies	retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,
Tursiops truncatus	ENSTTRG00000007433	1 retrocopy	retro_ttru_1821,