RetrogeneDB ID: retro_fcat_23

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D4:30718656..30719691(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000031480
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000029688
• Aliases: None
• Description: None

Sequence

>retro_fcat_23
ATGGCAACAGCCGGAGACGCGTTACTGCTACTGCGGCTCCCCGCGCTGTTCGAAACCAGCAAGCAGCTTCTGGACGAAGT
GGAAGCAGCGACTGAACCCACCGGTTCCCAGATAATTCAAGATAAGGTATTCAGGGGACTAGACCTCCTTAAGAAGGCTG
CTGAAATGTTATCGCAGCTCGACTTGTTCAGCCGAAATGAAGACTTGGAAGAGATTGCTTCCACAGACCTGAAGTACCTG
ATGGTCTCAGCTTTTCAAGGAGCGCTCGCCATGAAACAAGTCAACCCCAGCAAGCGTCTAGATCATTTGCAGTGGGCTCG
AGAACACTTTTTAAACTACTTAACTCAGTGCCAGTATTATCATGTGGCAGAGTTTGAGCTGCCCCAAACCAACTCAGCTG
ATAATAATACTGCTAGTTCCTCCATGGCGTGTCCTAGCCTCGTTGCTGTGGCATCTGAAAGACAGGCTAAAATAGAGAGA
TACAAGCAGAAGAAGGAGGTGGAGCATAGGTTGTTTGCACTGAAATCTGCTGTGGAAAGTGGTCAAGCAGATGATGAGTG
TGTTCGTGAATATTACCTTCTTCACCTTCGAAGGTGGATCGGTATTAGCTTAGAAGAGATTGAGAGCATTGACCAGGAGA
TGAAGATCCTGAGAGAAGACGACTCCTCAAAAGACGCATCAACTTCTTACTCATCTCCTCAGGACAGGCCTCCAATGAAA
CCCTTCGTTCTCACTCGGAATGTGGCCCAAGCCAAAGTATTTGGAGCTGGTTATCCAAGTCTGGCATCTATGACGGTGAA
TGACTGGTATGATCAGCATCAGAAATATGGAGCATTACCAGATCAGGGCATAGCCAAGATAACACCAGAGCTCAAAAGAG
CAGCTCAGCAACAGGAAGATCAGAAACAAAAGGAGGCAGAGGAGGAGGAAGAGGAGGAGGAGGAGGGGGAAGAAACACTC
CACAGAGTTCGGGAGTGGGATGACTGGAAGGACACCCATCCCAGAGGCTATGGCAACCGACAGAACATGGGTTAG

Alignment

ORF - retro_fcat_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.69 %
• Parental protein coverage: 94.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATAEDELLPPRLPELFETSKQLLDEVEVATEPTGSRIIQDKVFKGLDLLKKAVEMLAQLDLFSRNEDLE
          MATA.D.LL..RLP.LFETSKQLLDEVE.ATEPTGS.IIQDKVF.GLDLLKKA.EML.QLDLFSRNEDLE
Retrocopy MATAGDALLLLRLPALFETSKQLLDEVEAATEPTGSQIIQDKVFRGLDLLKKAAEMLSQLDLFSRNEDLE

Parental  EIASTDLKYLLVPAFQGALAMKQVNPSKRLDHLQWAREHFLNYLTQCQYYHVAEFELPKTKNNSPDNNTA
          EIASTDLKYL.V.AFQGALAMKQVNPSKRLDHLQWAREHFLNYLTQCQYYHVAEFELP.T..NS.DNNTA
Retrocopy EIASTDLKYLMVSAFQGALAMKQVNPSKRLDHLQWAREHFLNYLTQCQYYHVAEFELPQT--NSADNNTA

Parental  SSSMAYPSLVAMASQRQAKIKRYKQKKEVEHRLSALKSAVESGQADDERVREYYLLHLQRWIGISLEEIE
          SSSMA.PSLVA.AS.RQAKI.RYKQKKEVEHRL.ALKSAVESGQADDE.VREYYLLHL.RWIGISLEEIE
Retrocopy SSSMACPSLVAVASERQAKIERYKQKKEVEHRLFALKSAVESGQADDECVREYYLLHLRRWIGISLEEIE

Parental  SIDQEMKILREKDSSKQVPTSYSPRQDRPPMKPFILTRNMTQAKVFGAGYPSLASMTVNDWYDQHRKYGA
          SIDQEMKILRE.DSSK...TSYS..QDRPPMKPF.LTRN..QAKVFGAGYPSLASMTVNDWYDQH.KYGA
Retrocopy SIDQEMKILREDDSSKDASTSYSSPQDRPPMKPFVLTRNVAQAKVFGAGYPSLASMTVNDWYDQHQKYGA

Parental  LPDQGIAVTTPELKRTAQEHEDQEQKEEEDDEHTLHRARE
          LPDQGIA..TPELKR.AQ..EDQ.QKE.E..E.......E
Retrocopy LPDQGIAKITPELKRAAQQQEDQKQKEAEEEEEEEEEGEE

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	27.89 RPM
SRP017611_kidney	0.00 RPM	31.64 RPM
SRP017611_liver	0.00 RPM	14.25 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_23 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_23 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.

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007797	1 retrocopy	retro_btau_215,
Choloepus hoffmanni	ENSCHOG00000013654	3 retrocopies	retro_chof_1523, retro_chof_2206, retro_chof_438,
Callithrix jacchus	ENSCJAG00000012525	6 retrocopies	retro_cjac_111, retro_cjac_1225, retro_cjac_2278, retro_cjac_2968, retro_cjac_3417, retro_cjac_47,
Cavia porcellus	ENSCPOG00000010797	1 retrocopy	retro_cpor_44,
Dasypus novemcinctus	ENSDNOG00000014731	5 retrocopies	retro_dnov_1160, retro_dnov_2029, retro_dnov_2340, retro_dnov_2380, retro_dnov_678,
Echinops telfairi	ENSETEG00000003397	1 retrocopy	retro_etel_1637,
Felis catus	ENSFCAG00000029688	1 retrocopy	retro_fcat_23 ,
Homo sapiens	ENSG00000089289	5 retrocopies	retro_hsap_1317, retro_hsap_1848, retro_hsap_2766, retro_hsap_2919, retro_hsap_3059,
Gorilla gorilla	ENSGGOG00000027795	2 retrocopies	retro_ggor_112, retro_ggor_2020,
Myotis lucifugus	ENSMLUG00000004179	1 retrocopy	retro_mluc_316,
Macaca mulatta	ENSMMUG00000013929	2 retrocopies	retro_mmul_1545, retro_mmul_31,
Mus musculus	ENSMUSG00000031221	1 retrocopy	retro_mmus_169,
Nomascus leucogenys	ENSNLEG00000000747	5 retrocopies	retro_nleu_1399, retro_nleu_1653, retro_nleu_2334, retro_nleu_671, retro_nleu_828,
Otolemur garnettii	ENSOGAG00000011797	1 retrocopy	retro_ogar_110,
Pongo abelii	ENSPPYG00000020435	4 retrocopies	retro_pabe_1099, retro_pabe_1451, retro_pabe_2245, retro_pabe_2533,
Pan troglodytes	ENSPTRG00000021990	5 retrocopies	retro_ptro_1233, retro_ptro_1873, retro_ptro_1973, retro_ptro_1982, retro_ptro_901,
Pteropus vampyrus	ENSPVAG00000005483	1 retrocopy	retro_pvam_1462,
Rattus norvegicus	ENSRNOG00000026267	1 retrocopy	retro_rnor_311,
Tarsius syrichta	ENSTSYG00000006214	2 retrocopies	retro_tsyr_1537, retro_tsyr_2131,