RetrogeneDB ID: retro_fcat_1612

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: D4:16465486..16466214(-)
• Located in intron of: ENSFCAG00000011421

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED6
• Ensembl ID: ENSFCAG00000013091
• Aliases: None
• Description: mediator complex subunit 6 [Source:HGNC Symbol;Acc:19970]

Sequence

>retro_fcat_1612
ATGGCAGCCGTGGATATCCAAGATAAGCTGCTGGGAATCTCTTGGGTAGACTGTTCTGGATCCCCATTTTGAACTGTGGA
TACGTCCCGGATTACATTTCAGAAAGAAGTAATCCTTTCTACGACAGGACATGTAACGATGAAGTGGTCAAAATGCAGAG
GCTTACATTAAATCAAATGGTTGGAGTGGAATACATCTTTCTGCACGCTCAAGAGCCCATTCTTTTTTATCATTTGGAAG
CAACAGCGGCAGTCTTCTACCCAAGTTATCCCACTGGCTGGTTACTGTATCATTGCTGGAGTGATCTACCAGGCACCAGA
CCTGGGGTCAGTTGTAAACTCTAGGGTGCTTACTACAGTGCATGGCATTCAATCAGCTTTTGATGAAGCTGTGTTGTACT
GTCGATACCATCCTTCCCAGGTTATTGGTGGCACTTCAAAGATCGTGAAGAGCAAGATAAAGTCAAACCTAAAGCCAAAA
GGAAAGAAGAACCAAGCTCTATTTTTCAGAGACAACGTGTGCAGGCTTTGCTCCTGGACCTCAGGCAGAAATTTCCACCC
AAATTTGGGTAGCAAAAGTCTGGAGAAAAGCCTGTCCCAGTGGGTCAGACAAAGAAAGAGGCAGAGCCTATACCAGAGAC
TGTTAAATCTGAGGAAAAGGAGACCGTGAAGAACGTCCAACAGATAGGGAGCACGAAAGGCCCCCCGGAAAAACGAATGA
GGCTTCAG

Alignment

ORF - retro_fcat_1612 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.55 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAVDIRDNLLGISWVDSS-WIPILNSGSVLDYFSERSNPFYDRTCNNEVVKMQRLTLEHLNQMVGVEYI
          MAAVDI.D.LLGISWVD.S.WIPILN.G.V.DY.SERSNPFYDRTCN.EVVKMQRLT...LNQMVGVEYI
Retrocopy MAAVDIQDKLLGISWVDCS<WIPILNCGYVPDYISERSNPFYDRTCNDEVVKMQRLT---LNQMVGVEYI

Parental  LLHAQEPILF-IIRKQQRQSPTQVIPLADYYIIAGVIYQAPDLGSVINSRVLTAVHGIQSAFDEAMSYCR
          .LHAQEPILF.II.KQQRQS.TQVIPLA.Y.IIAGVIYQAPDLGSV.NSRVLT.VHGIQSAFDEA..YCR
Retrocopy FLHAQEPILF>IIWKQQRQSSTQVIPLAGYCIIAGVIYQAPDLGSVVNSRVLTTVHGIQSAFDEAVLYCR

Parental  YHPSK-GYWWHFKDHEEQDKVKPKAKRKEEPSSIFQRQRVDALLLDLRQKFPPKFVQQKSGEKPVPVDQT
          YHPS..GYWWHFKD.EEQDKVKPKAKRKEEPSSIFQRQRV.ALLLDLRQKFPPKF..QKSGEKPVPV.QT
Retrocopy YHPSQ<GYWWHFKDREEQDKVKPKAKRKEEPSSIFQRQRVQALLLDLRQKFPPKFG*QKSGEKPVPVGQT

Parental  KKEAEPIPETVKSEEKETTKNVQQIVSTKGPPEKRMRLQ
          KKEAEPIPETVKSEEKET.KNVQQI.STKGPPEKRMRLQ
Retrocopy KKEAEPIPETVKSEEKETVKNVQQIGSTKGPPEKRMRLQ

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	5.05 RPM
SRP017611_kidney	0.00 RPM	13.50 RPM
SRP017611_liver	0.00 RPM	6.87 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1612 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1612 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000013091	1 retrocopy	retro_fcat_1612 ,
Myotis lucifugus	ENSMLUG00000017357	1 retrocopy	retro_mluc_265,
Monodelphis domestica	ENSMODG00000007174	3 retrocopies	retro_mdom_1190, retro_mdom_524, retro_mdom_625,
Otolemur garnettii	ENSOGAG00000001311	1 retrocopy	retro_ogar_2597,
Ochotona princeps	ENSOPRG00000008957	1 retrocopy	retro_opri_820,
Sorex araneus	ENSSARG00000002553	1 retrocopy	retro_sara_495,
Tupaia belangeri	ENSTBEG00000002302	1 retrocopy	retro_tbel_2272,