RetrogeneDB ID: retro_fcat_1690

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: E2:28451811..28452369(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM49B
• Ensembl ID: ENSFCAG00000015625
• Aliases: None
• Description: family with sequence similarity 49, member B [Source:HGNC Symbol;Acc:25216]

Sequence

>retro_fcat_1690
TTCACACTCCGGTTGGACAAACTCAAGATGACAAATCCCTCCATACAGAATGATTTCTGTATTATAGAAGAACATTGAGT
CTTATGAGAATTAATAATGTTGCAGCAAAAGGAGAAAATGAAGTAAATAATAAATTGGCAAATCGACTGTCTTTGTTTTA
TGCTGGGGCAGTCTCAATGCTGAAAACCTGAAGTGATGCCACAACAAAATTTGTATCAGAAAATAAAAATTTACCAAAGA
AAATACCACAGATTGTCTAAGCACCACGGCTAGTGTATGCAGAGTCACGCTCGAAACACCGGAATACAGAAGCAGATTTA
CAAACGAAGAGACGGTGTCATTCTGCTTGAGGGTAATGTTGGGTGTCATAATACTTTATGACACATACAATTTAGTGGGA
GCATTTGCCAAAACTTCAAAAATTGATATGAAAGGTTGTATCAAAGTTCTTAAGGACCAATATCCCAATAGTGTAGAAAG
TCTTCTATTGCTCTCAGGTAAACAACAAAACATTTGAATGACGAGGCTATCTCCAAGCAAATCGGATCCATGCTGCAA

Alignment

ORF - retro_fcat_1690 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.68 %
• Parental protein coverage: 57.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  FTLRFDELKMTNPAIQNDFS-YYRRTLSRMRINNVPAEGENEVNNELANRMSLFYAEATPMLKTLSDATT
          FTLR.D.LKMTNP.IQNDF..YYRRTLS.MRINNV.A.GENEVNN.LANR.SLFYA.A..MLKT.SDATT
Retrocopy FTLRLDKLKMTNPSIQNDFC<YYRRTLSLMRINNVAAKGENEVNNKLANRLSLFYAGAVSMLKT*SDATT

Parental  KFVSENKNLPI-ENTTDCLSTMASVCRVMLETPEYRSRFTNEETVSFCLRVMVGVIILYDHVHPVGAFAK
          KFVSENKNLP..ENTTDCLST.ASVCRV.LETPEYRSRFTNEETVSFCLRVM.GVIILYD....VGAFAK
Retrocopy KFVSENKNLPK<ENTTDCLSTTASVCRVTLETPEYRSRFTNEETVSFCLRVMLGVIILYDTYNLVGAFAK

Parental  TSKIDMKGCIKVLKDQPPNSVEGLL-NALRYTTKHLNDETTSKQIRSMLQ
          TSKIDMKGCIKVLKDQ.PNSVE.LL..ALR.TTKHLNDE..SKQI.SMLQ
Retrocopy TSKIDMKGCIKVLKDQYPNSVESLL<IALR*TTKHLNDEAISKQIGSMLQ

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	75.64 RPM
SRP017611_kidney	0.00 RPM	20.20 RPM
SRP017611_liver	0.00 RPM	9.50 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1690 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1690 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009323	3 retrocopies	retro_dnov_1596, retro_dnov_1723, retro_dnov_896,
Dipodomys ordii	ENSDORG00000005160	1 retrocopy	retro_dord_381,
Echinops telfairi	ENSETEG00000015647	1 retrocopy	retro_etel_1299,
Felis catus	ENSFCAG00000015625	1 retrocopy	retro_fcat_1690 ,
Oryctolagus cuniculus	ENSOCUG00000013690	1 retrocopy	retro_ocun_953,
Procavia capensis	ENSPCAG00000002866	3 retrocopies	retro_pcap_293, retro_pcap_332, retro_pcap_40,
Sus scrofa	ENSSSCG00000005959	1 retrocopy	retro_sscr_978,