RetrogeneDB ID: retro_fcat_1139

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:159104931..159105276(+)
• Located in intron of: ENSFCAG00000012076

Retrocopy information

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

Parental gene information

• Parental gene symbol: H1FOO
• Ensembl ID: ENSFCAG00000000094
• Aliases: None
• Description: H1 histone family, member O, oocyte-specific [Source:HGNC Symbol;Acc:18463]

Sequence

>retro_fcat_1139
GAAAACAAAACAAATGGCAGAAGGAGCAGCCAAGATGGTGAAGCCCCCAGGAAAACAAAAGCTGAGAGTTGGAGTTCAAA
ATCCATGGTTCCCAAGGACAAGAATAGTGCTGCTTCTCCAGCCAAAAAGAAGGAAGACAAGGTCCCAAAAGAGGTTGTTG
CCCATGGGGTCAAGGAGGGGCCCAAAGCCAAGGCTCCTGCTACTCCTAGGGGTGGTGGGTCTAAGAGGGTGTCTGGACCC
CTGGCCAGAAAGACAGAGGCCCCAAGGGCTCAAGAAGGTCCAGCATGCCGTATCACCAAGGCCTCATCATTCAGATTGGC
CAGTAAGAAACTAGAAACTGAAAGC

Alignment

ORF - retro_fcat_1139 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.7 %
• Parental protein coverage: 54.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KSKVKGRRSNQDGEAHRKTKAGSQNSKSTVPKDKNSVASPAKKKENKVLKEVVACGAKVGPKAKATAPPR
          ..K..GRRS.QDGEA.RKTKA.S..SKS.VPKDKNS.ASPAKKKE.KV.KEVVA.G.K.GPKAKA.A.PR
Retrocopy ENKTNGRRSSQDGEAPRKTKAESWSSKSMVPKDKNSAASPAKKKEDKVPKEVVAHGVKEGPKAKAPATPR

Parental  ASGSKTVPAPLARKTGAPKGPRKP-CMPTKASSSKLASKKTEAES
          ..GSK.V..PLARKT.AP.....P.C..TKASS..LASKK.E.ES
Retrocopy GGGSKRVSGPLARKTEAPRAQEGPACRITKASSFRLASKKLETES

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1139 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1139 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017209	2 retrocopies	retro_cjac_3976, retro_cjac_981,
Felis catus	ENSFCAG00000000094	2 retrocopies	retro_fcat_1139 , retro_fcat_416,
Homo sapiens	ENSG00000178804	1 retrocopy	retro_hsap_2799,
Gorilla gorilla	ENSGGOG00000000735	1 retrocopy	retro_ggor_1946,
Myotis lucifugus	ENSMLUG00000025226	2 retrocopies	retro_mluc_1278, retro_mluc_1318,
Oryctolagus cuniculus	ENSOCUG00000029379	1 retrocopy	retro_ocun_1483,
Ochotona princeps	ENSOPRG00000010371	2 retrocopies	retro_opri_403, retro_opri_624,
Pongo abelii	ENSPPYG00000013414	1 retrocopy	retro_pabe_2225,
Pan troglodytes	ENSPTRG00000015380	1 retrocopy	retro_ptro_1896,
Pteropus vampyrus	ENSPVAG00000007110	1 retrocopy	retro_pvam_808,
Tursiops truncatus	ENSTTRG00000011276	1 retrocopy	retro_ttru_1111,