RetrogeneDB ID: retro_fcat_1234

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:188693544..188694252(-)
• Located in intron of: ENSFCAG00000022285

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC123
• Ensembl ID: ENSFCAG00000025803
• Aliases: None
• Description: cell division cycle 123 [Source:HGNC Symbol;Acc:16827]

Sequence

>retro_fcat_1234
AGTGTATTTCCTAGGCTTAACTAGAGTGCTCCAAGGGATGCAAACTGGATAGCAATGAACAGTTCTCTGAAATGTAAAAC
ATTCAGTGACAACTTTCCATTGTTCAAGAGTTCTGATTTCATCATTCTTGACTTCACTCAACCATTTATTCATTGCACTG
ATGATTCTCCAGATCCTCGTACAGAATATGAACTTGTTCTTCAACAATGGTGTGAATTAATTTCTGGGGCTGAGTTCTGA
TGTTTTGTTAAGGAAAACAAGCTTACTGGTATTTTTCAAAGGGACTATACACAATACTATGATCATATTTCTAAACAAAA
GGAAAAGATTTGCAGGTGCATACAAGAGTTTTCCAAGAAACACAGTATAAATTCTTAAATGAAGACTTTGTGTTGGATGT
ATCTAGAAACAGCAGTGGGAAGGTGTAGCTGATTGATTTTAATCCATTTGGTGAAGTTAACTGATTCACTGCTGTGTACT
TGGGAAGAGCTGATATCTGGGAGAAACTTAAAAGGTGATTTTAGTGAAAGAGATGCCCTGGAGCAGGATTCTCCAGCTTT
CAGCTGCACAAATAGTGAAGTAACAGTTCAACCCAGTCCCTATCTGAGTAACCAACTTCCCAAGGACTTTGTAGACCCGA
ACACTGGGGAGAATGCTCACAAACTCATAGATTTTCTTAAACTGAAAAGAAATCAGCAAAAGTCTAAC

Alignment

ORF - retro_fcat_1234 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.01 %
• Parental protein coverage: 70.54 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SVFPKLNWSAPRDAYWIAMNSSLKCKTLSDIFLLFKSSDFITRDFTQPFIHCTDDSPDPCIEYELVLRKW
          SVFP.LN.SAPRDA.WIAMNSSLKCKT.SD.F.LFKSSDFI..DFTQPFIHCTDDSPDP..EYELVL..W
Retrocopy SVFPRLN*SAPRDANWIAMNSSLKCKTFSDNFPLFKSSDFIILDFTQPFIHCTDDSPDPRTEYELVLQQW

Parental  CELIPGAEFRCFVKENKLIGISQRDYTQYYDHISKQKEEICRCIQDFFKK-HIQYKFLDEDFVFDVYRDS
          CELI.GAEF.CFVKENKL.GI.QRDYTQYYDHISKQKE.ICRCIQ..F.K...QYKFL.EDFV.DV.R.S
Retrocopy CELISGAEF*CFVKENKLTGIFQRDYTQYYDHISKQKEKICRCIQE-FSK<ETQYKFLNEDFVLDVSRNS

Parental  RGKVWLIDFNPFGEV-TDSLLFTWEELISGRNLKGDFSEGEGLEQDSPAFRCTNSEVTVQPSPYLSYRLP
          .GKV.LIDFNPFGEV.TDSLL.TWEELISGRNLKGDFSE...LEQDSPAF.CTNSEVTVQPSPYLS..LP
Retrocopy SGKV*LIDFNPFGEV>TDSLLCTWEELISGRNLKGDFSERDALEQDSPAFSCTNSEVTVQPSPYLSNQLP

Parental  KDFVDLSTGEDAHKLIDFLKLKRNQQEDD
          KDFVD..TGE.AHKLIDFLKLKRNQQ...
Retrocopy KDFVDPNTGENAHKLIDFLKLKRNQQKSN

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	0.11 RPM	48.89 RPM
SRP017611_kidney	0.31 RPM	63.17 RPM
SRP017611_liver	0.20 RPM	26.79 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1234 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1234 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000025803	1 retrocopy	retro_fcat_1234 ,
Myotis lucifugus	ENSMLUG00000010474	1 retrocopy	retro_mluc_1599,
Mustela putorius furo	ENSMPUG00000001047	1 retrocopy	retro_mputfur_1047,