RetrogeneDB ID: retro_fcat_72

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C2:120718428..120719064(-)
• Located in intron of: ENSFCAG00000003086

Retrocopy information

• Ensembl ID: ENSFCAG00000028193
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000029962
• Aliases: None
• Description: None

Sequence

>retro_fcat_72
ATGAACTGTCTGCCCTTCCTTCAATGCCATCAAATGATGCTGTTTGGAAAAATTTCCCAGCAGTTGTGTGGCTTAAAGAA
ACTCCCATGGTCATGTGACTGCAGATACTTCTGGGGCTGGTTGAATGCAGTGTTTCATAAAGTGGATTATGAACGCATCA
GGGATGTAGGACGCGATAGGGCAGCATCGGAGTGGCTGCTGCACTGTGGGGCCATGGTGCGCTACCACGGCCAGGAGAGG
TGGCAGAAGGACTACAACCGCCTCCCCACAGGACCTCTGGACAAGTACAAGGTTCAGGCAATTGATGCCACTGACTCTTG
TATCATGAGCATTGGATTTGATTACGTGGAGGGCCTACACCATGTTGAAAAAATAAGGCCACGCAAGTGTCATTATATCA
AGGAAGACTATTTGGAGAAACTTGGTAAACTTGAAAATTTACAAAAGAGTGTATTGGAAATGGAAATAATTTCATGTGGG
AATGTCACAGACAAAGGCATCATTGCTTTATATCACTCAAGAAACCTGAAATATTTATTGTTAAGTGATCTTCCTGGAGT
AAGAAAAAAAGAAAACCTTATCCGAGGCTTTAAGACAGCACTGCCTTCTCTGGAACTAAAATTAGACTTGAAGTAA

Alignment

ORF - retro_fcat_72 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.29 %
• Parental protein coverage: 98.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FVCLDQMMLFGKISQQLCGLKKLPWSCDCRYFWGWLNAVFNKVDYERIRDVGPDRAASEWLLRCGAMVRY
          F....QMMLFGKISQQLCGLKKLPWSCDCRYFWGWLNAVF.KVDYERIRDVG.DRAASEWLL.CGAMVRY
Retrocopy FLQCHQMMLFGKISQQLCGLKKLPWSCDCRYFWGWLNAVFHKVDYERIRDVGRDRAASEWLLHCGAMVRY

Parental  HGQERWQKDYNHLPTGPLDKYKIQAIDATDSCIMSIGFDYMEGLQHVEKIRLCKCHYIEDDCLEKLGKLE
          HGQERWQKDYN.LPTGPLDKYK.QAIDATDSCIMSIGFDY.EGL.HVEKIR..KCHYI..D.LEKLGKLE
Retrocopy HGQERWQKDYNRLPTGPLDKYKVQAIDATDSCIMSIGFDYVEGLHHVEKIRPRKCHYIKEDYLEKLGKLE

Parental  NLQKSVLEMEIISCGNVTDKGIIALYHLRNLKYLLLSDLPGVREKENIIRAFKTALPSLELKLDLK
          NLQKSVLEMEIISCGNVTDKGIIALYH.RNLKYLLLSDLPGVR.KEN.IR.FKTALPSLELKLDLK
Retrocopy NLQKSVLEMEIISCGNVTDKGIIALYHSRNLKYLLLSDLPGVRKKENLIRGFKTALPSLELKLDLK

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	0.34 RPM	3.33 RPM
SRP017611_kidney	0.21 RPM	5.77 RPM
SRP017611_liver	0.00 RPM	1.62 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_72 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_72 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009828	1 retrocopy	retro_amel_377,
Canis familiaris	ENSCAFG00000014285	1 retrocopy	retro_cfam_267,
Cavia porcellus	ENSCPOG00000014471	1 retrocopy	retro_cpor_740,
Felis catus	ENSFCAG00000029962	1 retrocopy	retro_fcat_72 ,
Loxodonta africana	ENSLAFG00000013773	1 retrocopy	retro_lafr_167,
Pteropus vampyrus	ENSPVAG00000006173	1 retrocopy	retro_pvam_539,
Sorex araneus	ENSSARG00000007707	1 retrocopy	retro_sara_694,