RetrogeneDB ID: retro_fcat_1162

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:19924752..19925186(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSFCAG00000021929
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL27A
• Ensembl ID: ENSFCAG00000008411
• Aliases: None
• Description: ribosomal protein L27a [Source:HGNC Symbol;Acc:10329]

Sequence

>retro_fcat_1162
CCACCCAGACTGAGGAAGATCTGGAAACTTCGGGGCCACGTGAGCCATGGCCATGGCCACATCGGCAAGCACCAGAAACA
CCCAGGAGGCCAGGGTCATGCTGGTGGCATGCATCATGACAGGATAAACCTTGACAAATATCACCCAGGCTACTTTGGAA
AAGTTGGTAGGAAGCATCACCACTTAGAGAGGAACCAGAGCTTCCACCCAACTGTCAACCTTGATCAACTGTGGACCTTG
GTCCTTGAGCAGACATACCCATGTCTGCCAAAAACAAGACAGGAGCTGGTCCTTGCATCGATGTGGTGCGATCGGGCTAC
TACAGAGTTTTGGGAAAGGACAAGCTCCCCAAACAGCCCGTCTTCGTGAAGGCCAAATTCTTCAGTAGAAGAGCCAAGGA
AAAGATTAAAGGTGTGGAGGGCACCTGTGTCCTG

Alignment

ORF - retro_fcat_1162 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.45 %
• Parental protein coverage: 97.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMRHYHLKRNQSFCP
          P.RLRK..KLRGHVSHGHG.IGKH.KHPGG.G.AGGMHH.RIN.DKYHPGYFGKVG..H.HL.RNQSF.P
Retrocopy PPRLRKIWKLRGHVSHGHGHIGKHQKHPGGQGHAGGMHHDRINLDKYHPGYFGKVGRKHHHLERNQSFHP

Parental  TVNLDKLWTLVSEQTRVNAAK-NKTGAAPIIDVVRSGYYKVLGKGKLPKQPVIVKAKFFSRRAEEKIKGV
          TVNLD.LWTLV.EQT.....K.NKTGA.P.IDVVRSGYY.VLGK.KLPKQPV.VKAKFFSRRA.EKIKGV
Retrocopy TVNLDQLWTLVLEQTYPCLPK<NKTGAGPCIDVVRSGYYRVLGKDKLPKQPVFVKAKFFSRRAKEKIKGV

Parental  GGACVL
          .G.CVL
Retrocopy EGTCVL

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	81.03 RPM
SRP017611_kidney	0.00 RPM	276.19 RPM
SRP017611_liver	0.00 RPM	198.34 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1162 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1162 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 15 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004205	15 retrocopies	retro_amel_1095, retro_amel_1160, retro_amel_1165, retro_amel_130, retro_amel_1311, retro_amel_1441, retro_amel_1673, retro_amel_393, retro_amel_450, retro_amel_497, retro_amel_521, retro_amel_693, retro_amel_752, retro_amel_966, retro_amel_989,
Bos taurus	ENSBTAG00000005349	2 retrocopies	retro_btau_126, retro_btau_45,
Canis familiaris	ENSCAFG00000006936	2 retrocopies	retro_cfam_145, retro_cfam_384,
Callithrix jacchus	ENSCJAG00000011775	1 retrocopy	retro_cjac_211,
Equus caballus	ENSECAG00000022469	1 retrocopy	retro_ecab_289,
Ficedula albicollis	ENSFALG00000000924	1 retrocopy	retro_falb_20,
Felis catus	ENSFCAG00000008411	13 retrocopies	retro_fcat_1162 , retro_fcat_1285, retro_fcat_1305, retro_fcat_1380, retro_fcat_1635, retro_fcat_1761, retro_fcat_1805, retro_fcat_1974, retro_fcat_469, retro_fcat_652, retro_fcat_673, retro_fcat_817, retro_fcat_907,
Loxodonta africana	ENSLAFG00000000425	2 retrocopies	retro_lafr_25, retro_lafr_50,
Myotis lucifugus	ENSMLUG00000016616	7 retrocopies	retro_mluc_113, retro_mluc_1253, retro_mluc_164, retro_mluc_2123, retro_mluc_2202, retro_mluc_47, retro_mluc_572,
Monodelphis domestica	ENSMODG00000007480	1 retrocopy	retro_mdom_575,
Mus musculus	ENSMUSG00000046364	1 retrocopy	retro_mmus_40,
Oryctolagus cuniculus	ENSOCUG00000005442	1 retrocopy	retro_ocun_12,
Rattus norvegicus	ENSRNOG00000014214	10 retrocopies	retro_rnor_132, retro_rnor_193, retro_rnor_1996, retro_rnor_2466, retro_rnor_253, retro_rnor_261, retro_rnor_334, retro_rnor_370, retro_rnor_565, retro_rnor_606,
Sus scrofa	ENSSSCG00000014569	9 retrocopies	retro_sscr_527, retro_sscr_574, retro_sscr_587, retro_sscr_588, retro_sscr_644, retro_sscr_668, retro_sscr_677, retro_sscr_769, retro_sscr_809,
Taeniopygia guttata	ENSTGUG00000008355	1 retrocopy	retro_tgut_18,