RetrogeneDB ID: retro_fcat_1998

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: X:79929060..79929695(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZFAND6
• Ensembl ID: ENSFCAG00000012931
• Aliases: None
• Description: zinc finger, AN1-type domain 6 [Source:HGNC Symbol;Acc:30164]

Sequence

>retro_fcat_1998
GTGCAACAGAGAAACATGGCTTAAGAAACTAATCACAGACAAGTTCTTATGCTTTGTTCTACTGGCTGCGGATTTTATGG
GAACCCTTGTACAAATGGCATGTGTTCAGTGTGCTATAAAGGCATCTTCAAAGATAGAATAGTAGTAATTGTAGAATCAG
CCCACCTTCGGCTTCTGTCAGTACTCTGTCCCAGTCTTTTCCGGTCCAGTGCGCAGAGGACAGCGTCCCTGACACGCGCA
GTTACCTCTAGACTCCACATCTGCATCCGGGCAGCCAAGCCCTGTATCAAATCAGTCACTTTTATCAGAATCTGTAGCAT
CTTCCCAAGTGGACAGTATGTCTGTGGACAAAGCAATCCCTGACACGGAAGACCTGCAAACTTCAGTATCAGATATGGCA
CAGCAGCCATCTGAAGAGCAAAGCAAGTCTCGTGAAAAACCAAAATAGAAAAAGAACGGCTGTTTCATGTGCAGGAAGAA
AGTAGGACTTACTGGGTTTGAATGCCGGTGTGGACATGTGTATTGTGGCGTACGCGGTTACTCAGACGTGCACAATTGCT
CGTACAATTACAAAGCTGATGCTGCGGAGAAAATCAGAAAAGAAAAACTCAGTAGTTGGTGAAAAGATCCAGAAG

Alignment

ORF - retro_fcat_1998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.11 %
• Parental protein coverage: 91.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VQQRNMAQETNHSQVPMLCSTGCGFYGNPRTNGMCSVCYK-EHLQRQNSSNGRISPPAASVGTLSESFPV
          VQQRNMA.ETNH.QV.MLCSTGCGFYGNP.TNGMCSVCYK..HLQR.NSSN.RISPP.ASV.TLS.SFPV
Retrocopy VQQRNMA*ETNHRQVLMLCSTGCGFYGNPCTNGMCSVCYK<RHLQR*NSSNCRISPPSASVSTLSQSFPV

Parental  QCAD-GSVP-DAQSPLDSTSASVQPSPVSNQSLLSESVASSQVDSTSVDKAIPDTEDLQASVSDTAQQPS
          QCA..G..P..AQ.PLDSTSAS.QPSPVSNQSLLSESVASSQVDS.SVDKAIPDTEDLQ.SVSD.AQQPS
Retrocopy QCAE<GQRP*HAQLPLDSTSASGQPSPVSNQSLLSESVASSQVDSMSVDKAIPDTEDLQTSVSDMAQQPS

Parental  EEQSKSLEKPKQKKNRCFMCRKKVGLTGFECRCGHVYCGVHRYSDVHNCSYNYKADAAEKIRKE-NPVVV
          EEQSKS.EKPK.KKN.CFMCRKKVGLTGFECRCGHVYCGV..YSDVHNCSYNYKADAAEKIRKE.N.V.V
Retrocopy EEQSKSREKPK*KKNGCFMCRKKVGLTGFECRCGHVYCGVRGYSDVHNCSYNYKADAAEKIRKE>NSV-V

Parental  GEKIQK
          GEKIQK
Retrocopy GEKIQK

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	9.07 RPM
SRP017611_kidney	0.00 RPM	17.00 RPM
SRP017611_liver	0.00 RPM	7.18 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1998 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1998 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 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012321	1 retrocopy	retro_btau_593,
Choloepus hoffmanni	ENSCHOG00000009491	2 retrocopies	retro_chof_1516, retro_chof_2072,
Felis catus	ENSFCAG00000012931	2 retrocopies	retro_fcat_1024, retro_fcat_1998 ,
Felis catus	ENSFCAG00000027317	1 retrocopy	retro_fcat_641,
Homo sapiens	ENSG00000086666	1 retrocopy	retro_hsap_4153,
Gorilla gorilla	ENSGGOG00000015621	1 retrocopy	retro_ggor_2790,
Loxodonta africana	ENSLAFG00000006722	1 retrocopy	retro_lafr_587,
Monodelphis domestica	ENSMODG00000019428	1 retrocopy	retro_mdom_685,
Nomascus leucogenys	ENSNLEG00000008870	1 retrocopy	retro_nleu_1387,
Pan troglodytes	ENSPTRG00000007361	2 retrocopies	retro_ptro_1375, retro_ptro_2824,
Rattus norvegicus	ENSRNOG00000013506	1 retrocopy	retro_rnor_2019,
Sus scrofa	ENSSSCG00000001779	2 retrocopies	retro_sscr_1206, retro_sscr_1207,