RetrogeneDB ID: retro_fcat_1316

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:157197653..157198064(+)
• Located in intron of: ENSFCAG00000027563

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC5L
• Ensembl ID: ENSFCAG00000028753
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 5-like [Source:HGNC Symbol;Acc:23366]

Sequence

>retro_fcat_1316
ATGGCCCAGAACTTCCATTGGGTGGACATCGACAAGTTTGATGAGAACAGGTTCCTGGGCAAGCAGGAGGAGGCAGCGGT
GGCCAGACCATGCCCGGACCCTGGTGAGGCGGATGGCCTTCTGCAGCAAGGGGGTGTGCTTCGAGCATTCCGTTCAGCCT
TGCAGAACTGTCCCATCAACACCAAGAATCAGGCCGTGAAGGAACGGTCCCAGAGCATGGTGCTGAAAGTACTTACAGAT
TTTAAGAGCAGAGCAATTGAGCAGGCTGTGCATTCACTGGATAGAAATGGCATTGACTTGCCAATCAAGTACATTTATAA
AGGGTTTGAGAAGCCCACAGAAAACAGCAGTGCAGTGTTACCCCAATGGCATGAAAAGGCATTAGCAGTAGGAGGACTAG
GCTCCATTATG

Alignment

ORF - retro_fcat_1316 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.66 %
• Parental protein coverage: 90.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSSRFRRVDIDEFDENKFVDEQEEAAAAAAEPGPDPSEVDGLLRQWDMLRAFHAALRNSPVNTKNQAVKE
          ....F..VDID.FDEN.F...QEEAA.A...P.PDP.E.DGLL.Q...LRAF..AL.N.P.NTKNQAVKE
Retrocopy MAQNFHWVDIDKFDENRFLGKQEEAAVA--RPCPDPGEADGLLQQGGVLRAFRSALQNCPINTKNQAVKE

Parental  RAQGVVLKVLTNFKSSEIEQAVQSLDRNGIDLLMKYIYKGFEKPTENSSAVLLQWHEKALAVGGLGSII
          R.Q..VLKVLT.FKS..IEQAV.SLDRNGIDL..KYIYKGFEKPTENSSAVL.QWHEKALAVGGLGSI.
Retrocopy RSQSMVLKVLTDFKSRAIEQAVHSLDRNGIDLPIKYIYKGFEKPTENSSAVLPQWHEKALAVGGLGSIM

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	11.25 RPM
SRP017611_kidney	0.31 RPM	6.39 RPM
SRP017611_liver	0.00 RPM	2.83 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1316 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1316 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016540	1 retrocopy	retro_amel_1798,
Callithrix jacchus	ENSCJAG00000006730	4 retrocopies	retro_cjac_1282, retro_cjac_1725, retro_cjac_2744, retro_cjac_3941,
Felis catus	ENSFCAG00000028753	1 retrocopy	retro_fcat_1316 ,
Macaca mulatta	ENSMMUG00000020628	2 retrocopies	retro_mmul_1650, retro_mmul_623,
Mustela putorius furo	ENSMPUG00000013924	1 retrocopy	retro_mputfur_1532,
Oryctolagus cuniculus	ENSOCUG00000002997	1 retrocopy	retro_ocun_518,
Procavia capensis	ENSPCAG00000013936	1 retrocopy	retro_pcap_274,
Pan troglodytes	ENSPTRG00000021362	1 retrocopy	retro_ptro_2185,
Rattus norvegicus	ENSRNOG00000014317	1 retrocopy	retro_rnor_2730,
Ictidomys tridecemlineatus	ENSSTOG00000007907	2 retrocopies	retro_itri_275, retro_itri_767,
Tupaia belangeri	ENSTBEG00000008398	1 retrocopy	retro_tbel_442,