RetrogeneDB ID: retro_fcat_804

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B2:137361281..137361920(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000023771
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSFCAG00000026943
• Aliases: None
• Description: voltage-dependent anion channel 2 [Source:HGNC Symbol;Acc:12672]

Sequence

>retro_fcat_804
ATATGTAACACACCGACTTACGGTGACCTAGGGAAGGCTGCCAAAGATGACTTCAACAAAGGCTATGGATTTGGCTCAGT
CAAAGTACGTCTGAGAACTAAGTCTTGTAGGGGAGTGGAATTTTCTACTTCTGGTCATGCTTACGCTGATACACAGAAAG
CGTCAGGCAACCTAGAGACCAAGTACAAGGTCTGTAGCTACGGACTTGCCTTCACCCAGAAATGGAACATAGACGATACT
CTTGGAACAGAAATCGCTTCACAGAATAAGTTGGCTGAAGGGTCGAAACGTACTCTCGATACCGTATTTGCACCGAACCC
AGGAAAGAAGAGTGGGAAATTGAAGGCCTCCTACAAATGGGATTGTTTCAGTCTCGGCGGTAATGTTGACGCAGATTTTT
CTGGACCGACCATCTTTGGCTTTGGAGGTTGGCTTGCTGGCTCCCAGACGAGTTTTGACACAGCCAGGTCCAAACTGCCA
CAGAATGGTGTCGCCCTGGGTTACACAGCTGCCGACTTCCAGCTGCACATGCATGTGAGTGATGGCCCTGAATTTGGAGG
GTCTGTCTACCAGGAGGTTAATGGGAAGACTGGAACATCAATAAGCGTTGCTTGGATGGCTGGCAGTAACAATACCCGG

Alignment

ORF - retro_fcat_804 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.17 %
• Parental protein coverage: 74.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCIPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFSTSGSSNTDTGKVTGTLETKYKWCEYGLT
          .C..P.Y.DLGKAA.D.FNKG.GFG.VK....TKSC.GVEFSTSG....DT.K..G.LETKYK.C.YGL.
Retrocopy ICNTPTYGDLGKAAKDDFNKGYGFGSVKVRLRTKSCRGVEFSTSGHAYADTQKASGNLETKYKVCSYGLA

Parental  FTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGKIKSSYKRECINLGCDVDFDFAGPAIHG
          FT.KWN.D.TLGTEIA.......G.K.T.DT.F.PN.GKKSGK.K.SYK..C..LG..VD.DF.GP.I.G
Retrocopy FTQKWNIDDTLGTEIASQNKLAEGSKRTLDTVFAPNPGKKSGKLKASYKWDCFSLGGNVDADFSGPTIFG

Parental  SAVFGYEGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVCEDLDTSVNLAW
          ...FG..GWLAG.Q..FD.A.SKL..N..A.GY...DFQLH..V.DG.EFGGS.YQ.V.....TS...AW
Retrocopy ---FG--GWLAGSQTSFDTARSKLPQNGVALGYTAADFQLHMHVSDGPEFGGSVYQEVNGKTGTSISVAW

Parental  TSGTNCTR
          ..G.N.TR
Retrocopy MAGSNNTR

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	88.15 RPM
SRP017611_kidney	0.00 RPM	128.41 RPM
SRP017611_liver	0.00 RPM	51.35 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_804 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_804 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 18 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012975	2 retrocopies	retro_btau_1252, retro_btau_1389,
Canis familiaris	ENSCAFG00000015398	1 retrocopy	retro_cfam_376,
Callithrix jacchus	ENSCJAG00000001145	1 retrocopy	retro_cjac_2385,
Felis catus	ENSFCAG00000008421	1 retrocopy	retro_fcat_1592,
Felis catus	ENSFCAG00000010075	2 retrocopies	retro_fcat_1985, retro_fcat_599,
Felis catus	ENSFCAG00000026943	3 retrocopies	retro_fcat_1385, retro_fcat_804 , retro_fcat_815,
Homo sapiens	ENSG00000165637	1 retrocopy	retro_hsap_2114,
Gorilla gorilla	ENSGGOG00000005861	5 retrocopies	retro_ggor_1677, retro_ggor_1949, retro_ggor_2934, retro_ggor_3036, retro_ggor_425,
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Myotis lucifugus	ENSMLUG00000007500	2 retrocopies	retro_mluc_1710, retro_mluc_2252,
Mustela putorius furo	ENSMPUG00000003268	1 retrocopy	retro_mputfur_354,
Mus musculus	ENSMUSG00000021771	1 retrocopy	retro_mmus_2667,
Otolemur garnettii	ENSOGAG00000030039	1 retrocopy	retro_ogar_2116,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Sarcophilus harrisii	ENSSHAG00000012048	1 retrocopy	retro_shar_325,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,