RetrogeneDB ID: retro_fcat_375

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A2:38738500..38739006(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YRDC
• Ensembl ID: ENSFCAG00000011018
• Aliases: None
• Description: yrdC domain containing (E. coli) [Source:HGNC Symbol;Acc:28905]

Sequence

>retro_fcat_375
CTCAAGGGCTGCAGCAAGGCCAAGCTGCCGCCTGTCTATCTGGGCCATGTGGCCGATGTCTACAGGGACTGCCATGTTGA
GCATATCCAAGGTGCTCCTGAAAGACTTATTATCAGAACCAGTGACCCTGGTGTTGGAAAGCTCCCAAGAGGTCAGTAAG
GACCTGAACCCCTTTACTCCTCTTGTAGGCACCTGGACTCCTATCATGGCTTCATGCAGGATTTGGCCTAGGTGTTTGAG
CAACACTTGCTCTCACCAGTACCAACCTTGACTCTTAGGCCAGTTCTCCAAATGTCAAGGAATTCCTGTACCTCTGGCCT
CAATCGTTGCCGGTCATTGATGGGGGACCAATTGGGGATGGCCAGAGCCCTGAGTACTGCTTGGGCTCAACTGTGGTTGA
CTTGTCTGTACTTGGAAAGTTTGGCATCATTCATCCAGGCTGTGCCCTGGAAAGTATTACATCCATCCTCCCACAGAAGT
ATGGGCTGTTCCCCTCACAGAGATCT

Alignment

ORF - retro_fcat_375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.22 %
• Parental protein coverage: 77.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LKLSGRTSSDPSFLDGSVSPLFSRYCHVRVPEG-LLKDLLPGPVTLVLERSEELNKDLNPFTRLVGIRIP
          LK........P..L.G.V.....R.CHV....G.LLKDLL..PVTLVLE.S.E..KDLNPFT.LVG...P
Retrocopy LKGCSKAKLPPVYL-GHVADVY-RDCHVEHIQG>LLKDLLSEPVTLVLESSQEVSKDLNPFTPLVGTWTP

Parental  D-HAFIQDLAQVFG-GPLALTSANLSSQASSLNVEEFQDLWPQLSLIIDGGPIGDGQSSEYRLGSTVVDL
          ..H.F.QDLA.VF....LALTS.NL.S.ASS.NV.EF..LWPQ....IDGGPIGDGQS.EY.LGSTVVDL
Retrocopy I<HGFMQDLA*VFE<ATLALTSTNLDS*ASSPNVKEFLYLWPQSLPVIDGGPIGDGQSPEYCLGSTVVDL

Parental  SVPGKFGIIRPGCALERTTAILQQKYGLLPSHGS
          SV.GKFGII.PGCALE..T.IL.QKYGL.PS..S
Retrocopy SVLGKFGIIHPGCALESITSILPQKYGLFPSQRS

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	8.38 RPM
SRP017611_kidney	0.00 RPM	5.46 RPM
SRP017611_liver	0.00 RPM	2.53 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_375 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_375 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 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001173	1 retrocopy	retro_amel_350,
Dasypus novemcinctus	ENSDNOG00000009111	2 retrocopies	retro_dnov_1774, retro_dnov_2232,
Equus caballus	ENSECAG00000022522	1 retrocopy	retro_ecab_534,
Felis catus	ENSFCAG00000011018	1 retrocopy	retro_fcat_375 ,
Homo sapiens	ENSG00000196449	2 retrocopies	retro_hsap_4199, retro_hsap_4289,
Gorilla gorilla	ENSGGOG00000007619	1 retrocopy	retro_ggor_2866,
Macropus eugenii	ENSMEUG00000005068	1 retrocopy	retro_meug_452,
Microcebus murinus	ENSMICG00000011953	1 retrocopy	retro_mmur_188,
Myotis lucifugus	ENSMLUG00000000955	1 retrocopy	retro_mluc_367,
Macaca mulatta	ENSMMUG00000005372	2 retrocopies	retro_mmul_1206, retro_mmul_1662,
Nomascus leucogenys	ENSNLEG00000011665	2 retrocopies	retro_nleu_1045, retro_nleu_1046,
Otolemur garnettii	ENSOGAG00000030474	2 retrocopies	retro_ogar_1107, retro_ogar_2342,
Pongo abelii	ENSPPYG00000001523	1 retrocopy	retro_pabe_3495,
Pan troglodytes	ENSPTRG00000000557	4 retrocopies	retro_ptro_2850, retro_ptro_2906, retro_ptro_2907, retro_ptro_2999,
Tupaia belangeri	ENSTBEG00000008863	1 retrocopy	retro_tbel_1817,
Tarsius syrichta	ENSTSYG00000005555	3 retrocopies	retro_tsyr_1108, retro_tsyr_1420, retro_tsyr_874,