RetrogeneDB ID: retro_fcat_2001

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:82314873..82315400(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNBP
• Ensembl ID: ENSFCAG00000028042
• Aliases: None
• Description: CCHC-type zinc finger, nucleic acid binding protein [Source:HGNC Symbol;Acc:13164]

Sequence

>retro_fcat_2001
ATGAGCAGCAATGAGTGTTTCCAGTGTGGATGATCTGGCCATTGGGCCCAGGAATGCCCTACTAGTGGAGGCTATGGTCA
TGGAATGAGAAGCTGTGGCAGAGGTGGTTTTACCCAGGTTAGAGGTTTCCAGTTTGTTTCCTCATCACATTCAGACATCT
GTTATCACTGTGTTGAGTCTGGTCATCTTGCCAAGGATCGTCATCTTCAGGAAGATGCCTGCTATAACTGTGATAGAGGT
GGTCACATTGCTAAGGAGTAGAAGGAGCTCAAGAGTGAGAACAATGTTGCTACAACTGTGGCAAACTAGGCCATCTGGCT
CGTGACTGTGACCATGCAGATGAACAGAAGTGCTATTCTTGTGGAGAATTTGGACACATTCAAAATGACTGCACCAAAAT
GAAGTGCTATGGGTGTGGTGAAACTGGTCACTCAGCCATCAATTGCAGTAAGACAGGTGAGATCAACTGTTACCACTGTG
GCGGGTCAAGGCACCTTGCACAGGAATGCATAATTGAAACCACAGCT

Alignment

ORF - retro_fcat_2001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.65 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSNECFKCGRSGHWARECPTGGGRGRGMRSRGRGGFTSDRGFQFVSSSLPDICYRCGESGHLAKDCDLQ
          MSSNECF.CG.SGHWA.ECPT.GG.G.GMRS.GRGGFT..RGFQFVSSS..DICY.C.ESGHLAKD..LQ
Retrocopy MSSNECFQCG*SGHWAQECPTSGGYGHGMRSCGRGGFTQVRGFQFVSSSHSDICYHCVESGHLAKDRHLQ

Parental  EDACYNCGRGGHIAKDCKEPKRE-REQCCYNCGKPGHLARDCDHADEQKCYSCGEFGHIQKDCTKVKCYR
          EDACYNC.RGGHIAK..KE.K.E....C.YNCGK.GHLARDCDHADEQKCYSCGEFGHIQ.DCTK.KCY.
Retrocopy EDACYNCDRGGHIAKE*KELKSE<EQCC-YNCGKLGHLARDCDHADEQKCYSCGEFGHIQNDCTKMKCYG

Parental  CGETGHVAINCSKTSEVNCYRCGESGHLARECTIEATA
          CGETGH.AINCSKT.E.NCY.CG.S.HLA.EC.IE.TA
Retrocopy CGETGHSAINCSKTGEINCYHCGGSRHLAQECIIETTA

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	154.94 RPM
SRP017611_kidney	0.00 RPM	226.42 RPM
SRP017611_liver	0.00 RPM	137.08 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_2001 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_2001 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 30 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015334	2 retrocopies	retro_amel_1285, retro_amel_1773,
Bos taurus	ENSBTAG00000012159	1 retrocopy	retro_btau_19,
Canis familiaris	ENSCAFG00000004320	2 retrocopies	retro_cfam_1272, retro_cfam_23,
Callithrix jacchus	ENSCJAG00000017430	1 retrocopy	retro_cjac_4079,
Cavia porcellus	ENSCPOG00000012816	2 retrocopies	retro_cpor_424, retro_cpor_94,
Dipodomys ordii	ENSDORG00000002919	1 retrocopy	retro_dord_569,
Equus caballus	ENSECAG00000009512	1 retrocopy	retro_ecab_1072,
Echinops telfairi	ENSETEG00000008408	5 retrocopies	retro_etel_12, retro_etel_1791, retro_etel_2192, retro_etel_237, retro_etel_583,
Felis catus	ENSFCAG00000028042	2 retrocopies	retro_fcat_1922, retro_fcat_2001 ,
Homo sapiens	ENSG00000169714	1 retrocopy	retro_hsap_50,
Gorilla gorilla	ENSGGOG00000010085	1 retrocopy	retro_ggor_2926,
Loxodonta africana	ENSLAFG00000002502	1 retrocopy	retro_lafr_49,
Macropus eugenii	ENSMEUG00000011699	1 retrocopy	retro_meug_55,
Myotis lucifugus	ENSMLUG00000012554	1 retrocopy	retro_mluc_141,
Macaca mulatta	ENSMMUG00000011585	1 retrocopy	retro_mmul_2505,
Mustela putorius furo	ENSMPUG00000017315	3 retrocopies	retro_mputfur_1465, retro_mputfur_1555, retro_mputfur_583,
Mus musculus	ENSMUSG00000030057	1 retrocopy	retro_mmus_230,
Nomascus leucogenys	ENSNLEG00000014482	1 retrocopy	retro_nleu_1986,
Oryctolagus cuniculus	ENSOCUG00000008696	2 retrocopies	retro_ocun_1626, retro_ocun_208,
Otolemur garnettii	ENSOGAG00000013898	1 retrocopy	retro_ogar_144,
Ochotona princeps	ENSOPRG00000005487	5 retrocopies	retro_opri_139, retro_opri_49, retro_opri_496, retro_opri_566, retro_opri_965,
Pongo abelii	ENSPPYG00000013423	1 retrocopy	retro_pabe_3658,
Pan troglodytes	ENSPTRG00000015369	1 retrocopy	retro_ptro_3131,
Pteropus vampyrus	ENSPVAG00000015070	1 retrocopy	retro_pvam_908,
Rattus norvegicus	ENSRNOG00000010239	2 retrocopies	retro_rnor_207, retro_rnor_727,
Sorex araneus	ENSSARG00000011874	1 retrocopy	retro_sara_397,
Sarcophilus harrisii	ENSSHAG00000017132	1 retrocopy	retro_shar_666,
Ictidomys tridecemlineatus	ENSSTOG00000000173	1 retrocopy	retro_itri_113,
Tarsius syrichta	ENSTSYG00000004344	1 retrocopy	retro_tsyr_1889,
Vicugna pacos	ENSVPAG00000007138	1 retrocopy	retro_vpac_548,