RetrogeneDB ID: retro_fcat_105

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:45895100..45896696(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000030093
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PKM
• Ensembl ID: ENSFCAG00000000653
• Aliases: None
• Description: Pyruvate kinase isozyme M1/M2 [Source:UniProtKB/Swiss-Prot;Acc:P11979]

Sequence

>retro_fcat_105
ATGTCAAAGCCCCATAGTGATGTCGGGACTGCCTTCATTCAGACCCAGCAGCTGTACGCAGCCATGGCTGACACGTTCTT
GGAGCACACGTGCCGCCTGGACATTGACTCGCCACCCATCACGGCCCGTAACACTGGCATCATCTGTACCATCTGTCCGG
CTTCCCGATCTGTGGAGATATTGAAAGAGATGATTAAATCTGGAATGAATGTGGCTCGTCTGAACTTCTCTCATGGAACT
CATGAGTACCATGCTGAGACCATCAAGAATGTGCGTGCAGCCACGGAAAGCTTTGCTTCTGACCCCATTCGTTACCAGCC
AGTTGCTGTGGCCCTGGACACCAAAGGACCTGAGATCCGAACTGGGCTCATCAAGGGCAGTGGCACCGCAGAGGTGGAGC
TGAAGAAAGGAGCCACTCTCAAGATCACCTTGGACAATGCCTACATGGAAAAATGCGATGAGAATGTCCTGTGGCTGGAC
TACAAGAACATTTGCAAGGTGGTGGAAGTGGGCAGCAAGGTCTACGTGGACGATGGGCTTATCTCTCTGTTGGTGAAGGA
GAAAGGTGCTGACTTCCTGGTGACAGAGGTGGAGAATGGTGGCTCCCTGGGGAGCAAGAAGGGTGTGAACCTTCCTGGGG
CTGCTGTGGACTTGCCTGCTGTGTCAGAAAAGGACATCCAGGATCTGAAATTTGGGGTAGAGCAGGATGTAGATATGGTG
TTTGCATCTTTCATCCGCAAGGCATCTGATGTCCATGAAGTTAGAAAGGTCCTGGGAGAAAAAGGAAAGAACATCAAGAT
AATCAGCAAAATTGAGAATCATGAGGGAGTTCGGAGGTTTGATGAAATCCTGGAAGCCAGCGATGGGATCATGGTGGCTC
GTGGTGATCTAGGCATTGAGATTCCTGCAGAGAAGGTCTTCCTTGCTCAGAAGATGATGATTGGGAGGTGCAACCGAGCT
GGGAAGCCTGTCATCTGTGCGACGCAGATGCTGGAGAGCATGATCAAGAAGCCCCGTCCCACCAGAGCTGAGGGCAGTGA
TGTGGCCAATGCGGTCTTGGATGGAGCCGACTGTATCATGCTTTCTGGAGAGGTAGTCAAAGGGGACTACCCCCTGGAGG
CTGTTCGCATGCAGCACCTGATTGCCCGTGAGGCAGAGGCTGCCATCTACCACTTGCAATTATTTGAGGAACTCCGCCGC
CTGGAGCCCATTACCAGCGACCCTACCGAAGCCGCCGCCGTGGGCGCTGTGGAGGCCTCGTTCAAGTGCTGCAGTGGGGC
CATAATCGTCCTCACCAAGTCTGGCAGGTCTGCTCACCAGGTGGCCAGATACCGCCCCCGCGCCCCCATCATTGCTGTGA
CTCGGAATCACCAGACTGCCCGCCAGGCCCACCTGTACCTCGGCATCTTCCCTGTGGTGTCTAAGGACCCAGTGCAGGAG
GCCTGGGCTGAGGATGTGGACCTTCGAGTGAACTTGGCCATGAATGTTGGCAAGGCCCGAGGCTTCTTCAAGAAGGGAGA
TGTGGTCATTGTGCTGACCGGGTGGCGCCCTGGCTCTGGCTTCACCAATACCATGCGTGTAGTGCCTGTGCCATGA

Alignment

ORF - retro_fcat_105 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKPHSDVGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVEILKEMIKSGMN
          MSKPHSDVGTAFIQTQQL.AAMADTFLEH.CRLDIDSPPITARNTGIICTI.PASRSVEILKEMIKSGMN
Retrocopy MSKPHSDVGTAFIQTQQLYAAMADTFLEHTCRLDIDSPPITARNTGIICTICPASRSVEILKEMIKSGMN

Parental  VARLNFSHGTHEYHAETIKNVRAATESFASDPIRYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
          VARLNFSHGTHEYHAETIKNVRAATESFASDPIRY.PVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
Retrocopy VARLNFSHGTHEYHAETIKNVRAATESFASDPIRYQPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL

Parental  KITLDNAYMEKCDENVLWLDYKNICKVVEVGSKVYVDDGLISLLVKEKGADFLVTEVENGGSLGSKKGVN
          KITLDNAYMEKCDENVLWLDYKNICKVVEVGSKVYVDDGLISLLVKEKGADFLVTEVENGGSLGSKKGVN
Retrocopy KITLDNAYMEKCDENVLWLDYKNICKVVEVGSKVYVDDGLISLLVKEKGADFLVTEVENGGSLGSKKGVN

Parental  LPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRF
          LPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRF
Retrocopy LPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRF

Parental  DEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVAN
          DEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVAN
Retrocopy DEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVAN

Parental  AVLDGADCIMLSGETAKGDYPLEAVRMQHLIAREAEAAMFHRKLFEELVRGSSHSTDLMEAMAMGSVEAS
          AVLDGADCIMLSGE..KGDYPLEAVRMQHLIAREAEAA..H..LFEEL.R......D..EA.A.G.VEAS
Retrocopy AVLDGADCIMLSGEVVKGDYPLEAVRMQHLIAREAEAAIYHLQLFEELRRLEPITSDPTEAAAVGAVEAS

Parental  YKCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRNHQTARQAHLYRGIFPVVCKDPVQEAWAEDVDLRV
          .KC...A.IVLT.SGRSAHQVARYRPRAPIIAVTRNHQTARQAHLY.GIFPVV.KDPVQEAWAEDVDLRV
Retrocopy FKCCSGAIIVLTKSGRSAHQVARYRPRAPIIAVTRNHQTARQAHLYLGIFPVVSKDPVQEAWAEDVDLRV

Parental  NLAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP
          NLAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP
Retrocopy NLAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP

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	12.97 RPM	417.66 RPM
SRP017611_kidney	7.11 RPM	68.84 RPM
SRP017611_liver	0.61 RPM	10.61 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_105 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_105 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 13 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013504	1 retrocopy	retro_chof_1430,
Callithrix jacchus	ENSCJAG00000018473	1 retrocopy	retro_cjac_236,
Felis catus	ENSFCAG00000000653	1 retrocopy	retro_fcat_105 ,
Homo sapiens	ENSG00000067225	2 retrocopies	retro_hsap_210, retro_hsap_3418,
Gorilla gorilla	ENSGGOG00000005062	1 retrocopy	retro_ggor_281,
Macropus eugenii	ENSMEUG00000004506	3 retrocopies	retro_meug_1482, retro_meug_2043, retro_meug_912,
Macaca mulatta	ENSMMUG00000023454	1 retrocopy	retro_mmul_183,
Mus musculus	ENSMUSG00000032294	8 retrocopies	retro_mmus_1402, retro_mmus_1678, retro_mmus_1754, retro_mmus_2065, retro_mmus_2066, retro_mmus_2636, retro_mmus_3509, retro_mmus_854,
Nomascus leucogenys	ENSNLEG00000013869	3 retrocopies	retro_nleu_1859, retro_nleu_2319, retro_nleu_2716,
Pongo abelii	ENSPPYG00000006613	3 retrocopies	retro_pabe_2834, retro_pabe_3645, retro_pabe_429,
Pan troglodytes	ENSPTRG00000007246	2 retrocopies	retro_ptro_2322, retro_ptro_335,
Rattus norvegicus	ENSRNOG00000011329	6 retrocopies	retro_rnor_1120, retro_rnor_2050, retro_rnor_2253, retro_rnor_2703, retro_rnor_515, retro_rnor_830,
Sarcophilus harrisii	ENSSHAG00000010300	1 retrocopy	retro_shar_90,