RetrogeneDB ID: retro_fcat_1888

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: JH409009.1:129429..130318(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOT2
• Ensembl ID: ENSFCAG00000025552
• Aliases: None
• Description: glutamic-oxaloacetic transaminase 2, mitochondrial [Source:HGNC Symbol;Acc:4433]

Sequence

>retro_fcat_1888
ATGGCTTTCCTGCACGCCAGCCATGTTCTGTCTGAGGTTGCCACCACCTTCCACTGAGGCCTTGCTGCCGTGACTTCTGC
CAGAGCCAGCTCCTGGTGGACCCGTGTTGGGATGGGGCCCCCAGATCCCATCCTGGGAGTCACATAAACCTTTAAGAGAG
GTGTCAACAGCAAAAAAAAAATGGTAGTTGGTGCCTACTGAGATGATAACGGAAAGCCTTATGTGCCTTATAGTGTTCAG
AAGGCAAAGGCCCAGATTACTGCCAAAAAATTTGACAAGGAATACCTGTCCATCGCAGGATTTGGTAAATTTTGTAAGGC
ATCTGCAGAACTAGCCCTGAGTGAGAACAATGAAGTGTTGAAAAGTAGCTGGTATGTCACCATACAGACCATTTCTGGAA
ATGCGGCCTTGATGATTGGAGCCAGTTTTTTTAAAAGATTTTTTAAGTTAAGCCAAGATGTCTTTCTGCCCAACCATCTT
GGAGAAATTACACACCCATCTTCAGGGATGCTGGTGTGCAATTACATGATTATCAATACTAAGGCCCCAAGACATGCAGC
TCTGACTTTATAGGCACTATAGAGGACATTTTGAAAATGCCACAGCAAAGTGTTCTCCTTCATGCTTGTGTCCACAGTCC
AGGAGTGGACCCTTACCCTGATAAATGGAAGGAAGCAGCAACAGTGATGAAGAAAAACAATTTCTTTGTGTCGTTTTACA
TGTCCTACCAAGGCTTTGCCAGTGGTGATGGCAAAAAGATGCCTGGGCTGTATATCACTTCATCTTCATCAAACAGGGAA
TTACTGTTTGTCTCTGCCAATCCTATACCAAGAACATTGGCTTATACAGTGAGCATGTGGGAGCCTTCATTGTGGTTTGC
CAAGATGCT

Alignment

ORF - retro_fcat_1888 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.19 %
• Parental protein coverage: 69.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALLHTGRVLSGVAAAFHPGLAAAASARASSWWTHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDD
          MA.LH...VLS.VA..FH.GLAA..SARASSWWT.V.MGPPDPILGVT..FKR..NS......VGAY.DD
Retrocopy MAFLHASHVLSEVATTFH*GLAAVTSARASSWWTRVGMGPPDPILGVT*TFKRGVNSXXXXV-VGAY*DD

Parental  NGKPYVLPSVRKAEAQIAAKNLDKEYLPIAGLAEFCKASAELALGENNEVLKSSRYVTVQTISGTGALRI
          NGKPYV..SV.KA.AQI.AK..DKEYL.IAG...FCKASAELAL.ENNEVLKSS.YVT.QTISG..AL.I
Retrocopy NGKPYVPYSVQKAKAQITAKKFDKEYLSIAGFGKFCKASAELALSENNEVLKSSWYVTIQTISGNAALMI

Parental  GASFLQRFFKFSRDVYLP-KPSWGNHTPVFRDAGMQLHSYRYYDPKTCGFDFTGAIEDISKMPQQSVLLL
          GASF..RFFK.S.DV.LP..PSW.N.TP.FRDAG.QLH.Y.Y..PKTC..DF.G.IEDI.KMPQQSV.LL
Retrocopy GASFFKRFFKLSQDVFLP<QPSWRNYTPIFRDAGVQLHDYQY*GPKTCSSDFIGTIEDILKMPQQSV-LL

Parental  HACAHNPTGVDPRPEQWKEIATVVKKNNLFAFFDMAYQGFASGDG-NKDAWAVRH--FIEQGINVCLCQS
          HAC.H.P.GVDP.P..WKE.ATV.KKNN.F..F.M.YQGFASGDG..KDAWAV.H..FI.QGI.VCLCQS
Retrocopy HACVHSP-GVDPYPDKWKEAATVMKKNNFFVSFYMSYQGFASGDG<QKDAWAVYHFIFIKQGITVCLCQS

Parental  YAKNMGLYGERVGAFTVVCKDA
          Y.KN.GLY.E.VGAF.VVC.DA
Retrocopy YTKNIGLYSEHVGAFIVVCQDA

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	116.38 RPM
SRP017611_kidney	0.00 RPM	87.70 RPM
SRP017611_liver	0.00 RPM	122.42 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1888 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1888 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 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017346	3 retrocopies	retro_amel_1805, retro_amel_815, retro_amel_846,
Canis familiaris	ENSCAFG00000008357	2 retrocopies	retro_cfam_586, retro_cfam_816,
Callithrix jacchus	ENSCJAG00000011234	1 retrocopy	retro_cjac_2916,
Equus caballus	ENSECAG00000016504	1 retrocopy	retro_ecab_694,
Felis catus	ENSFCAG00000025552	3 retrocopies	retro_fcat_1068, retro_fcat_1888 , retro_fcat_381,
Gorilla gorilla	ENSGGOG00000005767	3 retrocopies	retro_ggor_2912, retro_ggor_449, retro_ggor_774,
Macaca mulatta	ENSMMUG00000006000	1 retrocopy	retro_mmul_1337,
Mustela putorius furo	ENSMPUG00000004862	1 retrocopy	retro_mputfur_567,
Pongo abelii	ENSPPYG00000007413	3 retrocopies	retro_pabe_3640, retro_pabe_823, retro_pabe_901,
Rattus norvegicus	ENSRNOG00000011782	1 retrocopy	retro_rnor_2695,