RetrogeneDB ID: retro_fcat_642

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B1:107899538..107900150(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEMO1
• Ensembl ID: ENSFCAG00000001385
• Aliases: None
• Description: mediator of cell motility 1 [Source:HGNC Symbol;Acc:14014]

Sequence

>retro_fcat_642
CAACAGCGAGGTTAGCTTTCACAAGCACAGTCTACGGAAAGAGCTGCGAGAGCCATTATTGCACCCCATGCAGGGTATGC
AGTACTGTGGATCTTGTGCTGCCCATGCTTACAAACAAGTAGATCCATCTACTACCCGGAGAATTTTCACCCTGATGCCT
TCTCATCCTGTGCCTCTCTTGTGATGTGTACTTTCCAGTGTGCATATATAGAGAACACCTCTGTGTGACCTTCATATTGA
CCAAAAGATTTTTGAGAACTATGGAAGATAGGAATGTTTGAACACATGTCTCTGTAGACACATGAAAATGAACACAGTGT
TGAAATGCATTTGCCTTATACAGGTAAAGCCATGGAAAGCCAGGAGGATGAGTTTACTATTATTCCTATACTAGTTGGAG
CTTTGAGTGAATCAAAAGAACAGGAATTTGGAAAACTCTTCAGCAAATACCCAGCAGATCCTAGTAATCTCTTTGTGGTT
TCTTCTGATTTCTTCCACTGGAGCCAAAGATTCTGTTACAGTTACTATGATGAACCTCAGGAGAAGATTTATAGATCCAT
TGAGTATCTAGATAAAATGGGCATGAGTATTATAGACCAGTTAGACACTATA

Alignment

ORF - retro_fcat_642 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.64 %
• Parental protein coverage: 73.65 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QLEGWLSQVQSTKRPARAIIAPHAGYT-YCGSCAAHAYKQVDPSITRRIFILGPSHHVPLSRCALSSVDI
          Q..G.LSQ.QST.R.ARAIIAPHAGY..YCGSCAAHAYKQVDPS.TRRIF.L.PSH.VPL..C.LSSV.I
Retrocopy QQRG*LSQAQSTERAARAIIAPHAGYA>YCGSCAAHAYKQVDPSTTRRIFTLMPSHPVPLL*CVLSSVHI

Parental  YRTPLYDLRIDQKIYG-ELWKTGMFERMSLQTDEDEHSIEMHLPYTAKAMESHKDEFTIIPVLVGALSES
          .RTPL.DL.IDQKI...ELWK.GMFE.MSL.T.E.EHS.EMHLPYT.KAMES..DEFTIIP.LVGALSES
Retrocopy *RTPLCDLHIDQKIFE<ELWKIGMFEHMSL*THENEHSVEMHLPYTGKAMESQEDEFTIIPILVGALSES

Parental  KEQEFGKLFSKYLADPSNLFVVSSDFCHWGQRFRYSYYDESQGEIYRSIEHLDKMVMSIIEQLDPV
          KEQEFGKLFSKY.ADPSNLFVVSSDF.HW.QRF.YSYYDE.Q..IYRSIE.LDKM.MSII.QLD..
Retrocopy KEQEFGKLFSKYPADPSNLFVVSSDFFHWSQRFCYSYYDEPQEKIYRSIEYLDKMGMSIIDQLDTI

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	13.54 RPM
SRP017611_kidney	0.00 RPM	7.73 RPM
SRP017611_liver	0.00 RPM	7.78 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_642 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_642 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	ENSAMEG00000007771	1 retrocopy	retro_amel_1500,
Equus caballus	ENSECAG00000019946	1 retrocopy	retro_ecab_401,
Echinops telfairi	ENSETEG00000007994	1 retrocopy	retro_etel_561,
Felis catus	ENSFCAG00000001385	1 retrocopy	retro_fcat_642 ,
Homo sapiens	ENSG00000162959	2 retrocopies	retro_hsap_2507, retro_hsap_3522,
Myotis lucifugus	ENSMLUG00000016108	1 retrocopy	retro_mluc_1923,
Mus musculus	ENSMUSG00000058704	1 retrocopy	retro_mmus_834,
Nomascus leucogenys	ENSNLEG00000015577	1 retrocopy	retro_nleu_488,
Oryctolagus cuniculus	ENSOCUG00000005878	3 retrocopies	retro_ocun_1441, retro_ocun_1663, retro_ocun_928,
Otolemur garnettii	ENSOGAG00000010975	3 retrocopies	retro_ogar_1860, retro_ogar_2049, retro_ogar_3050,
Pongo abelii	ENSPPYG00000012511	1 retrocopy	retro_pabe_2910,