RetrogeneDB ID: retro_fcat_1477

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D2:32541169..32541614(+)
• Located in intron of: ENSFCAG00000027361

Retrocopy information

• Ensembl ID: ENSFCAG00000004706
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000004260
• Aliases: None
• Description: None

Sequence

>retro_fcat_1477
CTGCCCCACAGGTTTATCAAGGAAACCCAGCGTTTGCTGGCGGAAACAGTCCCTGGCATTAGAGCAGAACGAGATGACAG
CAGTGCCCGTTATTTTCATGTGGTCATTGCTGGCCCCCAGGGTTTTCCTTTTGAGGGAGGGACTTTTAAACTTGAACTAT
TCCTTCCAGAAGAATACCCATTGGCAGCCCCTAAAGTGTGTTTTGTGACCAAAATTTATCATCCTAATGTAGACAAATTG
GAAGAATATGTTTAGATATTTTGAAAGATAAGTGGTCCCCTGTACTGCAGATCTGCACGGTTCTGCTGTTGACCTCGGCC
TTGTTAAGTGCTCCCAATCCAGATGATGCATTAGCAAGGATGTAGCAGAGCAGTGGAAGACCAATGAAGCCCAAGCCATA
GAAACAGCTAGAGCATGGACTAGGCTGTGTGCCATGAACAATATT

Alignment

ORF - retro_fcat_1477 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.11 %
• Parental protein coverage: 98.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IPRVFSKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGTFKLELFLPEEYPMAAPKVRFMT
          .P..F.KETQRLLAE.VPGI.AE.D.S.ARYFHVVIAGPQ..PFEGGTFKLELFLPEEYP.AAPKV.F.T
Retrocopy LPHRFIKETQRLLAETVPGIRAERDDSSARYFHVVIAGPQGFPFEGGTFKLELFLPEEYPLAAPKVCFVT

Parental  KIYHPNVDKL-GRICLDILKDKWSPALQIRTVLLSIQALLSAPNPDDPLA-NDVAEQWKTNEAQAIETAR
          KIYHPNVDKL.GRICLDILKDKWSP.LQI.TVLL...ALLSAPNPDD.LA..DVAEQWKTNEAQAIETAR
Retrocopy KIYHPNVDKL<GRICLDILKDKWSPVLQICTVLLLTSALLSAPNPDDALA<KDVAEQWKTNEAQAIETAR

Parental  AWTRLYAMNNI
          AWTRL.AMNNI
Retrocopy AWTRLCAMNNI

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	40.63 RPM
SRP017611_kidney	0.00 RPM	18.24 RPM
SRP017611_liver	0.00 RPM	8.29 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1477 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1477 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 19 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009833	1 retrocopy	retro_amel_507,
Canis familiaris	ENSCAFG00000006177	1 retrocopy	retro_cfam_196,
Callithrix jacchus	ENSCJAG00000002979	8 retrocopies	retro_cjac_141, retro_cjac_2121, retro_cjac_3142, retro_cjac_3148, retro_cjac_3216, retro_cjac_3241, retro_cjac_3329, retro_cjac_425,
Cavia porcellus	ENSCPOG00000008581	5 retrocopies	retro_cpor_1548, retro_cpor_230, retro_cpor_24, retro_cpor_655, retro_cpor_750,
Echinops telfairi	ENSETEG00000001882	5 retrocopies	retro_etel_1008, retro_etel_1417, retro_etel_1593, retro_etel_1661, retro_etel_2136,
Felis catus	ENSFCAG00000004260	2 retrocopies	retro_fcat_1477 , retro_fcat_1598,
Homo sapiens	ENSG00000177889	3 retrocopies	retro_hsap_1392, retro_hsap_17, retro_hsap_3124,
Loxodonta africana	ENSLAFG00000028985	1 retrocopy	retro_lafr_57,
Macropus eugenii	ENSMEUG00000002944	7 retrocopies	retro_meug_1236, retro_meug_1287, retro_meug_1453, retro_meug_1473, retro_meug_162, retro_meug_2009, retro_meug_31,
Myotis lucifugus	ENSMLUG00000009982	2 retrocopies	retro_mluc_2166, retro_mluc_453,
Macaca mulatta	ENSMMUG00000020634	3 retrocopies	retro_mmul_1587, retro_mmul_234, retro_mmul_72,
Monodelphis domestica	ENSMODG00000009451	2 retrocopies	retro_mdom_133, retro_mdom_1485,
Oryctolagus cuniculus	ENSOCUG00000011287	1 retrocopy	retro_ocun_100,
Otolemur garnettii	ENSOGAG00000034461	7 retrocopies	retro_ogar_1502, retro_ogar_2178, retro_ogar_406, retro_ogar_408, retro_ogar_566, retro_ogar_584, retro_ogar_732,
Pongo abelii	ENSPPYG00000004832	4 retrocopies	retro_pabe_113, retro_pabe_1152, retro_pabe_2580, retro_pabe_3326,
Pan troglodytes	ENSPTRG00000005297	3 retrocopies	retro_ptro_2112, retro_ptro_3253, retro_ptro_956,
Sorex araneus	ENSSARG00000005945	3 retrocopies	retro_sara_174, retro_sara_438, retro_sara_695,
Sarcophilus harrisii	ENSSHAG00000007776	1 retrocopy	retro_shar_105,
Tarsius syrichta	ENSTSYG00000008800	5 retrocopies	retro_tsyr_1476, retro_tsyr_1754, retro_tsyr_207, retro_tsyr_348, retro_tsyr_5,