RetrogeneDB ID: retro_fcat_177

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: A1:129061663..129062230(+)
• Located in intron of: ENSFCAG00000015128

Retrocopy information

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

Parental gene information

• Parental gene symbol: YIPF5
• Ensembl ID: ENSFCAG00000031350
• Aliases: None
• Description: Yip1 domain family, member 5 [Source:HGNC Symbol;Acc:24877]

Sequence

>retro_fcat_177
AACACAGATTTCTACCAGACAAGTTACAGCATTGATGACCAATCACAGCAATCCTATGACTATGGAGGAAGTGGAGAACC
CTATAGCAAACAGTTTGCTGGCTATGACTACTCACAGCAAGGCCAATTTGTCCCTCTAGACATGAGGCAGCCATAACAGC
CACATACTGGGCCAATTTTCCAGCCAACTCAGGCATACACTCTAACACATTAGCTTATCTATGGAAAACACTTTGAGGAT
AAGCCACCTTTATTAGAAGAATCAGGTATCACTTGTGACCACATCTGGCAAAAAACATGAACAGTGTTACATCCATTACA
AGTGGAAGATGGCAGCATCATGAATGTGACTGATTTGGCACAACCAATGGTTTTTTGCCTTGCCTTTGGAGCCACATTGT
TACTGGCTGGCAAAATCCAGTTTGGCTATGTATGTGGCATAAGTGCACTTGGATGTCTAGGAATGTTTTTGTCTACTAAA
CTGAGTATGACAGGTGTTTCATTTGGTTGTGTGGCAAGTGTCCGTGGATACTGTCTTCTTCCGATGATCCTACTTTCCAG
CTCTGCA

Alignment

ORF - retro_fcat_177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.68 %
• Parental protein coverage: 74.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NTDFYQTSYSIDDHSQQSYDYGGSGGPYSKQYAGYDYSQQGRFVPPDMMQPQQPYTGQIFQPTQAYTPTT
          NTDFYQTSYSIDD.SQQSYDYGGSG.PYSKQ.AGYDYSQQG.FVP.DM.QP.QP.TG.IFQPTQAYT..T
Retrocopy NTDFYQTSYSIDDQSQQSYDYGGSGEPYSKQFAGYDYSQQGQFVPLDMRQP*QPHTGPIFQPTQAYT-LT

Parental  PQPFYGNNFEDEPPLLEELGINFDHIWQKTLTVLHPLKVADGSIMNETDLAGPMVFCLAFGATLLLAGKI
          ....YG..FED.PPLLEE.GI..DHIWQKT.TVLHPL.V.DGSIMN.TDLA.PMVFCLAFGATLLLAGKI
Retrocopy H*LIYGKHFEDKPPLLEESGITCDHIWQKT*TVLHPLQVEDGSIMNVTDLAQPMVFCLAFGATLLLAGKI

Parental  QFGYVYGISAIGCLGMFCLLNLMSMTGVSFGCVASVLGYCLLPMILLSSFA
          QFGYV.GISA.GCLGMF.L....SMTGVSFGCVASV.GYCLLPMILLSS.A
Retrocopy QFGYVCGISALGCLGMF-LSTKLSMTGVSFGCVASVRGYCLLPMILLSSSA

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	51.76 RPM
SRP017611_kidney	0.00 RPM	32.36 RPM
SRP017611_liver	0.00 RPM	48.83 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_177 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_177 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010135	1 retrocopy	retro_amel_489,
Dasypus novemcinctus	ENSDNOG00000014497	1 retrocopy	retro_dnov_16,
Felis catus	ENSFCAG00000031350	1 retrocopy	retro_fcat_177 ,
Myotis lucifugus	ENSMLUG00000011143	3 retrocopies	retro_mluc_2549, retro_mluc_521, retro_mluc_750,
Otolemur garnettii	ENSOGAG00000001543	2 retrocopies	retro_ogar_2657, retro_ogar_2803,
Tarsius syrichta	ENSTSYG00000008071	1 retrocopy	retro_tsyr_16,