RetrogeneDB ID: retro_fcat_1852

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:48226177..48227184(-)
• Located in intron of: ENSFCAG00000005022

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPN
• Ensembl ID: ENSFCAG00000004978
• Aliases: None
• Description: centromere protein N [Source:HGNC Symbol;Acc:30873]

Sequence

>retro_fcat_1852
ATGGATGAAACTGTTGCCACGTTTATCATGAGGACCATCTTGAAAATCCCAATGACTGAAATGATGAAAATCCTCAAAGC
CTGGGATTTTTTGTCTGCAAATCAACTGCAGACCATAAGCTTCCGGCAGAGAAAGGAATCTCTCGTTCAGGACTTGGTTC
TGCTCTGTGAGAATAAGTGTGCAAGTCTCCACGACACAGCCCTTTTAGACATCATTTATACTCAATTTCATCGGCACCAG
AAAGTTTGGGATGTTTTTCAAATGAGTAAAGAACCAGGTGAAGATGCTGACCTTTTTTGATACGGAACAATTCAAAAGTT
CATTTGAGAAAATTCTTCGGAGAGCATTAAAAAATGTGAGGGTCAGCTTCAGAGACGCTGAGGAGAATGCAGTACGGATC
TGAATTGACTGGGGAACGCAGCATAGAAAGTCAAACCAGTACAAACCTGTCTGTGTGCTGTATTACTCCCAGACTCCCTA
CACCTTCACTTCCTTCTGCCACCTGAAGAGCAATATACCCCTTCTGGGTCAGGCACTGACAATGGCTAGCAATCACCGTA
AGATTGTGAAAATGGACCTCAGAAGCCAGTATGTGGACTCTCTGAAGGCTATTGTTTTCAAACCGTATAGTCAGACCTTT
GAAACTCACAACTCCACCAAACCTCTACAAGAAACCCTTGAGCCGGACATGCACACGGATTCAAGGACCATTCATGAAAA
CAGAATCGAAAAAGAGAGAGTCCGGAGAGTGACTCAAGAAACTTTTGGAGACTATCCTCCGCCAAGACTAGAATTTGCAC
AATATAAGCTTGAAACGAAATTCAAAAGTGACTTCCATGGGGGCATCTTGGCTGAGAGAAAAGAGCCCCTCCGGTGCCTA
ATGAAGTTCTCTAGCCTGCATCTTCTGGAAGCACTGAAATCCTTAGCACCAGCTGGTATTGCAGTCACACCACTTTCTCC
ATTGCTCACCCAATAAGGGAATGAATTATTTTAAAATCAGAGATAAA

Alignment

ORF - retro_fcat_1852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDETVAEFIKRTILKIPMTEMMTILKAWDFLPENQLQTVNFRQRKESLVQDLVLLCESKRASLRDAALLD
          MDETVA.FI.RTILKIPMTEMM.ILKAWDFL..NQLQT..FRQRKESLVQDLVLLCE.K.ASL.D.ALLD
Retrocopy MDETVATFIMRTILKIPMTEMMKILKAWDFLSANQLQTISFRQRKESLVQDLVLLCENKCASLHDTALLD

Parental  IIYTQFHQHQKVWDVFQMSKEPGEDVDLF-DMERFKSSFEKILRRALKNVTVSFRDAEENAVWIRIAWGT
          IIYTQFH.HQKVWDVFQMSKEPGED.DLF.D.E.FKSSFEKILRRALKNV.VSFRDAEENAV.I.I.WGT
Retrocopy IIYTQFHRHQKVWDVFQMSKEPGEDADLF>DTEQFKSSFEKILRRALKNVRVSFRDAEENAVRI*IDWGT

Parental  QYRKPNQYKPVYVVYYSQTPYAFTSFCHLKSNTPLLSQALTVASNHHKIVKMDLRSRYLDSLKAIVFKQY
          Q.RK.NQYKPV.V.YYSQTPY.FTSFCHLKSN.PLL.QALT.ASNH.KIVKMDLRS.Y.DSLKAIVFK.Y
Retrocopy QHRKSNQYKPVCVLYYSQTPYTFTSFCHLKSNIPLLGQALTMASNHRKIVKMDLRSQYVDSLKAIVFKPY

Parental  NQKFETHNSTMPLQETLELDMHSIVDSRIIHENKIEKERVQRVTQETFGDYPQPRLEFAQYKLETKFRSD
          .Q.FETHNST.PLQETLE.DMH...DSR.IHEN.IEKERV.RVTQETFGDYP.PRLEFAQYKLETKF.SD
Retrocopy SQTFETHNSTKPLQETLEPDMHT--DSRTIHENRIEKERVRRVTQETFGDYPPPRLEFAQYKLETKFKSD

Parental  FHGGILAERKEPLRCLIKFSSPHLLEALKSLAPAGIADAPLSPL-LTCIPNKGMNYFKIRDK
          FHGGILAERKEPLRCL.KFSS.HLLEALKSLAPAGIA.....PL.L.C.PNKGMNYFKIRDK
Retrocopy FHGGILAERKEPLRCLMKFSSLHLLEALKSLAPAGIA---VTPL>LHCSPNKGMNYFKIRDK

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	0.46 RPM	1.26 RPM
SRP017611_kidney	0.21 RPM	7.21 RPM
SRP017611_liver	0.00 RPM	5.46 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1852 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1852 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
Bos taurus	ENSBTAG00000011635	1 retrocopy	retro_btau_1101,
Felis catus	ENSFCAG00000004978	1 retrocopy	retro_fcat_1852 ,
Homo sapiens	ENSG00000166451	2 retrocopies	retro_hsap_2146, retro_hsap_2291,
Oryctolagus cuniculus	ENSOCUG00000000024	3 retrocopies	retro_ocun_1676, retro_ocun_1806, retro_ocun_528,
Sarcophilus harrisii	ENSSHAG00000002111	1 retrocopy	retro_shar_331,
Ictidomys tridecemlineatus	ENSSTOG00000007345	1 retrocopy	retro_itri_1431,
Tupaia belangeri	ENSTBEG00000000039	2 retrocopies	retro_tbel_2049, retro_tbel_3055,