RetrogeneDB ID: retro_rnor_541

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:253955772..253956303(+)
• Located in intron of: ENSRNOG00000014768

Retrocopy information

• Ensembl ID: ENSRNOG00000014782
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pebp1
• Ensembl ID: ENSRNOG00000001136
• Aliases: Pebp1, HCNP, Pbp, Rkip
• Description: Phosphatidylethanolamine-binding protein 1 Hippocampal cholinergic neurostimulating peptide [Source:UniProtKB/Swiss-Prot;Acc:P31044]

Sequence

>retro_rnor_541
CTGGCCACCAACATCAGACAGTGGGCCTAGCCGCTGTGCCTACAGGAGGTGGACGAGCCACTCCAGCACGCTCTGAGGGT
CGACTACCCTCAGAGTGACGATGGACAAGCTGGGCAAAGTGCTGACGCCCACCCAGGTCATGAACAGGCCGAGCAGTATT
TCATGGGATGGCCTTAATCCAGGGAAGCTCTACACCCTGGTCCTCACAGACCCCCTCGATGCTCCCAGCAGGAAGGGCCC
CAAATTCAGGGAGTGGCACCAATTCCTGGTGGTCAACATTAAGGGCAACGACACTAGCAATGGCACTGTCCTCTCGGACT
ACGTGGGCTCCGGGCCTCCCAATGGCACAGGTCTGCACCGCTACGTCTGGCTGGTGTACGAGCAGGAGCAGCCTCTGAGC
TGTGACAGAGCCCATCCTCAGCCGCAGGTCTGGAGACAACCGCGGCAAGTTCAAGGTGGAGAACCTTCCGCAAGAAGTAC
CACCAGGGAGCCCCCGTGGCCGGTGCGTGCTACCAGGCAGAGTGGGATGAC

Alignment

ORF - retro_rnor_541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.68 %
• Parental protein coverage: 93.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAADISQWAGPLSLQEVDEPPQHALRVDYGG-VTVDELGKVLTPTQVMNRPSSISWDGLDPGKLYTLVLT
          .A..I.QWA.PL.LQEVDEP.QHALRVDY...VT.D.LGKVLTPTQVMNRPSSISWDGL.PGKLYTLVLT
Retrocopy LATNIRQWA*PLCLQEVDEPLQHALRVDYPQ>VTMDKLGKVLTPTQVMNRPSSISWDGLNPGKLYTLVLT

Parental  DP-DAPSRKDPKFREWHHFLVVNMKGNDISSGTVLSEYVGSGPPKDTGLHRYVWLVYEQEQPLNCD-EPI
          DP.DAPSRK.PKFREWH.FLVVN.KGND.S.GTVLS.YVGSGPP..TGLHRYVWLVYEQEQPL.CD.EPI
Retrocopy DPLDAPSRKGPKFREWHQFLVVNIKGNDTSNGTVLSDYVGSGPPNGTGLHRYVWLVYEQEQPLSCD>EPI

Parental  LSNKSGDNRGKFKVE-SFRKKYHLGAPVAGTCFQAEWDD
          LS..SGDNRGKFKVE..FRKKYH.GAPVAG.C.QAEWDD
Retrocopy LSRRSGDNRGKFKVE>TFRKKYHQGAPVAGACYQAEWDD

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	218.35 RPM
SRP017611_kidney	0.00 RPM	275.85 RPM
SRP017611_liver	0.00 RPM	184.63 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_541 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_541 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016143	2 retrocopies	retro_amel_1355, retro_amel_754,
Bos taurus	ENSBTAG00000018115	2 retrocopies	retro_btau_1183, retro_btau_705,
Canis familiaris	ENSCAFG00000009910	1 retrocopy	retro_cfam_526,
Callithrix jacchus	ENSCJAG00000009314	2 retrocopies	retro_cjac_1410, retro_cjac_818,
Erinaceus europaeus	ENSEEUG00000003689	1 retrocopy	retro_eeur_292,
Felis catus	ENSFCAG00000002277	3 retrocopies	retro_fcat_1317, retro_fcat_1360, retro_fcat_299,
Homo sapiens	ENSG00000089220	3 retrocopies	retro_hsap_1456, retro_hsap_2288, retro_hsap_492,
Gorilla gorilla	ENSGGOG00000013281	3 retrocopies	retro_ggor_1121, retro_ggor_1701, retro_ggor_461,
Myotis lucifugus	ENSMLUG00000002259	7 retrocopies	retro_mluc_103, retro_mluc_1612, retro_mluc_1742, retro_mluc_2357, retro_mluc_2373, retro_mluc_984, retro_mluc_998,
Macaca mulatta	ENSMMUG00000005098	4 retrocopies	retro_mmul_1621, retro_mmul_2272, retro_mmul_328, retro_mmul_442,
Mustela putorius furo	ENSMPUG00000002861	3 retrocopies	retro_mputfur_1228, retro_mputfur_1361, retro_mputfur_223,
Mus musculus	ENSMUSG00000032959	4 retrocopies	retro_mmus_138, retro_mmus_1857, retro_mmus_2314, retro_mmus_542,
Nomascus leucogenys	ENSNLEG00000000322	1 retrocopy	retro_nleu_1966,
Oryctolagus cuniculus	ENSOCUG00000008395	2 retrocopies	retro_ocun_1329, retro_ocun_1900,
Otolemur garnettii	ENSOGAG00000001740	1 retrocopy	retro_ogar_2750,
Pongo abelii	ENSPPYG00000005011	2 retrocopies	retro_pabe_1202, retro_pabe_241,
Pan troglodytes	ENSPTRG00000005512	3 retrocopies	retro_ptro_1621, retro_ptro_371, retro_ptro_992,
Rattus norvegicus	ENSRNOG00000001136	3 retrocopies	retro_rnor_1223, retro_rnor_46, retro_rnor_541 ,
Ictidomys tridecemlineatus	ENSSTOG00000004085	2 retrocopies	retro_itri_1603, retro_itri_961,
Tupaia belangeri	ENSTBEG00000000177	2 retrocopies	retro_tbel_272, retro_tbel_2728,
Tursiops truncatus	ENSTTRG00000000658	1 retrocopy	retro_ttru_1164,