RetrogeneDB ID: retro_rnor_2160

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:99488028..99488605(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Zcchc9
• Ensembl ID: ENSRNOG00000014927
• Aliases: None
• Description: zinc finger CCHC domain-containing protein 9 [Source:RefSeq peptide;Acc:NP_001013174]

Sequence

>retro_rnor_2160
TTCATGTAATACCTGGAACAGAGCTCACAGATGCTTCACAGTGGAGAGCTGATAGGATCAGACAAGCAGGAAGTAAGAGG
AGAAATTGCAGCTGTCCTTAAAGGACAATAAACAGGAAGGAAGGCAGCTAAAAAGACAAGCAGCAAAGAAAAGGGCAATG
GTAATGGTATATTTCCACTGTAAAAAAACCTGGCTATGGGATTACTAATTGCCCAAGTGAACTATAATGTGGAGATATGG
ACACTGGTATTTACCACTACTGCAGGTCCATGGAGAACAACATTGCGACCTGCAGAGGTGAATTCGGTGAATTTTCCTTT
GCCAAGGCTTTTTTCTGTGGAGAAATGGGACACCTTTCTAGGTACTGTCCTGGTAGTGCCGAAGGAGCCTACATTGATAG
TGGCAGCTGTAAACTCTGTGGCTCTGTTGGACGTTTTAAGAAGGTTGCCCTGAAGATCAGAATTTAAATCCAATCACCAC
AGTTGGTTGCTGTGCAAAAGGAATGAATGCAGACCACAAAGATATTATGAATGTGACCAAACCGCAGAAAGCTTAAACGA
AAGTACCCAAAGTTGTT

Alignment

ORF - retro_rnor_2160 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.0 %
• Parental protein coverage: 71.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FMEYLKQSSQVLHNGQLIAADSREVR-EEIAVALKKDSRREGRRLKRQAAKKNAMVC--FHCRQ-PGHGI
          FM.YL.QSSQ.LH.G.LI..D..EVR.E.....LK.D...EGR.LKRQAAKK.AMV...FHC...PG.GI
Retrocopy FM*YLEQSSQMLHSGELIGSDKQEVR>EKLQLSLK-DNKQEGRQLKRQAAKKRAMVMVYFHCKK>PGYGI

Parental  ADCPAVLESQDMGTGICYRCGSTEHEMTKCRANVDPALGEFPFAKCFVCGEMGHLSRSCPDNTKGVYADG
          ..CP..L...DM.TGI...C.S.E.....CR.......GEF.FAK.F.CGEMGHLSR.CP....G.Y.D.
Retrocopy TNCPSEL*CGDMDTGIYHYCRSMENNIATCRGE----FGEFSFAKAFFCGEMGHLSRYCPGSAEGAYIDS

Parental  GGCKLCGSVEHFKK-DCPENQNSDRIITVGRWAKGMSADHEDVLDVPKPQKPKTKVPKVV
          G.CKLCGSV..FKK..CPE.QN...I.TVG..AKGM.ADH.D...V.KPQK..TKVPKVV
Retrocopy GSCKLCGSVGRFKK<GCPEDQNLNPITTVGCCAKGMNADHKDIMNVTKPQKA*TKVPKVV

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	23.37 RPM
SRP017611_kidney	0.00 RPM	19.12 RPM
SRP017611_liver	0.00 RPM	11.56 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2160 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2160 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2160 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005265	1 retrocopy	retro_btau_1095,
Canis familiaris	ENSCAFG00000008703	2 retrocopies	retro_cfam_1547, retro_cfam_675,
Choloepus hoffmanni	ENSCHOG00000005268	3 retrocopies	retro_chof_140, retro_chof_2143, retro_chof_268,
Callithrix jacchus	ENSCJAG00000019486	4 retrocopies	retro_cjac_1236, retro_cjac_2906, retro_cjac_3528, retro_cjac_909,
Echinops telfairi	ENSETEG00000003838	2 retrocopies	retro_etel_325, retro_etel_880,
Homo sapiens	ENSG00000131732	1 retrocopy	retro_hsap_1799,
Gorilla gorilla	ENSGGOG00000013790	1 retrocopy	retro_ggor_706,
Microcebus murinus	ENSMICG00000016266	5 retrocopies	retro_mmur_125, retro_mmur_1325, retro_mmur_1341, retro_mmur_606, retro_mmur_819,
Myotis lucifugus	ENSMLUG00000001886	1 retrocopy	retro_mluc_799,
Macaca mulatta	ENSMMUG00000020655	1 retrocopy	retro_mmul_797,
Mus musculus	ENSMUSG00000021621	1 retrocopy	retro_mmus_1920,
Otolemur garnettii	ENSOGAG00000002543	6 retrocopies	retro_ogar_1467, retro_ogar_2125, retro_ogar_2426, retro_ogar_2941, retro_ogar_3076, retro_ogar_459,
Pongo abelii	ENSPPYG00000015604	1 retrocopy	retro_pabe_1476,
Pan troglodytes	ENSPTRG00000017047	2 retrocopies	retro_ptro_1205, retro_ptro_602,
Rattus norvegicus	ENSRNOG00000014927	2 retrocopies	retro_rnor_1164, retro_rnor_2160 ,
Sorex araneus	ENSSARG00000008580	2 retrocopies	retro_sara_216, retro_sara_78,
Sarcophilus harrisii	ENSSHAG00000014504	1 retrocopy	retro_shar_734,
Ictidomys tridecemlineatus	ENSSTOG00000001407	2 retrocopies	retro_itri_422, retro_itri_696,
Tarsius syrichta	ENSTSYG00000012423	1 retrocopy	retro_tsyr_244,
Tursiops truncatus	ENSTTRG00000013796	1 retrocopy	retro_ttru_819,