RetrogeneDB ID: retro_fcat_416

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A3:13726112..13726716(+)
• Located in intron of: None

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_416
ATGACAGCCCCCAGGAGGCCTGGTGAGGCCAAGGAGAAGGGCCCCAAACAACCAACGGACGCAAAGAAGGACCCTCCCAA
CCCAGGTGAGGTGAAAAGGGGACCCATGAAGCCAGGAGAGGCGAGGACAAGGTTTCTCCCAAACCAGGTGCAGCCGAGAA
GGCTCCCAAGAAAGGCAGCCAGACCAAAGACCAAGAGGCAAGACTGAGTGAGGCCAGGAAGGCCTCCCAGCAGCCCGACA
AGGCCAGCCAGACCCTTCCTAGTGCCCCTGGCTCCAGTGGGAAGTCCAAGGTCAAAGGCGCAAGGAGAAGCCAAGACGGT
GAGGCCCACATGAACACAAAAGCTAGGAGTCAGAGTTCAAAATCCACGGTTCCCAAGGGCAAGATTAGTGACGCTTCTCC
AGCCAAAAAGAAGGAAAGCGAGGTCCCTAAAGAGGCTGTTGCCCAAGGGGCCAACGTGGGGCCCAGAGTCAAGGCTGCTG
CTCCTCTTGGGGGCGGTGGGTCTAAGACAATGCCTGAACACCTGGCCAGGAAGACAGAGGCCCCCAAGGGCCCAGAAGGC
CTAGCATGCCCACACAGGCCTCCTCATCCACATTGACCTATAAG

Alignment

ORF - retro_fcat_416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.08 %
• Parental protein coverage: 97.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTAPRKPSEAKEKGPKKPREAKKDPPNPGEVKRGPKKP-REARTGPTKLDAAKEKAPKKGSQTKDQEARL
          MTAPR.P.EAKEKGPK.P..AKKDPPNPGEVKRGP.KP.R...........A.EKAPKKGSQTKDQEARL
Retrocopy MTAPRRPGEAKEKGPKQPTDAKKDPPNPGEVKRGPMKP<RRGEDKVSPKPGAAEKAPKKGSQTKDQEARL

Parental  SEAKKASQQPDKATQDLPSATGPRGKSKVKGRRSNQDGEAHRKTKAGSQNSKSTVPKDKNSVASPAKKKE
          SEA.KASQQPDKA.Q.LPSA.G..GKSKVKG.R..QDGEAH..TKA.SQ.SKSTVPK.K.S.ASPAKKKE
Retrocopy SEARKASQQPDKASQTLPSAPGSSGKSKVKGARRSQDGEAHMNTKARSQSSKSTVPKGKISDASPAKKKE

Parental  NKVLKEVVACGAKVGPKAKATAPPRASGSKTVPAPLARKTGAPK-GPRKPCMPTKASSSKLASK
          ..V.KE.VA.GA.VGP..KA.AP....GSKT.P..LARKT.APK.GPR.P.MPT.ASSS.L..K
Retrocopy SEVPKEAVAQGANVGPRVKAAAPLGGGGSKTMPEHLARKTEAPK<GPRRPSMPTQASSSTLTYK

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_416 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_416 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,