RetrogeneDB ID: retro_fcat_1813

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:40579101..40579603(+)
• Located in intron of: ENSFCAG00000015513

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB6
• Ensembl ID: ENSFCAG00000008036
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 6 [Source:HGNC Symbol;Acc:9543]

Sequence

>retro_fcat_1813
ATGGCGGCCACCTTAGAATCTGGTGGAGGAGCGGGGTCTGTCCCAGCCTGGGGTCCCGAGGCTATTGCCCCCGACTGGGA
AAGCCAGGAAGTCTCCACAGGGACCACTATCATGGCCATACAATTTGAAGGGGGTGTGGTTCTCGAAGCCGGCTCCAGAA
CTACCACTGGGTCCTACATCGCCAATTGAGTGACTGACAAGCTGACCCCTATCCATGACCGTATCTTCTGCTGCCGCTCA
GGCTCAGCAGCAGATACCCAGGCAGTAGCTGATGCTGTCACGTATCAGCTTGGTTTCCACAGCATTGAGCTAAATGAGCC
TCTGCTGCTGTACACAGCCGCCAGCCTCTTTAAGGAGATGTGTTACCTATACCGGGAAGAATTGATGGCAGGAATCATCA
CTGCAGGCTGGGACCTCCAAGAAGGAGGCCAGGTGTACTCGGTGCCCCTGGGGGGGTATGATGGTAAGGCAGTCCTTTGC
CATTGGGGGCTCTGGGAGCTCC

Alignment

ORF - retro_fcat_1813 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.48 %
• Parental protein coverage: 69.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAATLVSAGGAGSVPAWGPEAIAPDWESREVSTGTTIMAVQFEGGVVLGADSRTTTGSYIANRVTDKLTP
          MAATL.S.GGAGSVPAWGPEAIAPDWES.EVSTGTTIMA.QFEGGVVL.A.SRTTTGSYIAN.VTDKLTP
Retrocopy MAATLESGGGAGSVPAWGPEAIAPDWESQEVSTGTTIMAIQFEGGVVLEAGSRTTTGSYIAN*VTDKLTP

Parental  IHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGWDPQ
          IHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEP.L..TAASLFKEMCY.YRE.LMAGII.AGWD.Q
Retrocopy IHDRIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPLLLYTAASLFKEMCYLYREELMAGIITAGWDLQ

Parental  EGGQVYSVPM-GGMMVRQSFAIGGSGSS
          EGGQVYSVP..GGMMVRQSFAIGGSGSS
Retrocopy EGGQVYSVPL>GGMMVRQSFAIGGSGSS

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	0.11 RPM	14.12 RPM
SRP017611_kidney	0.00 RPM	27.10 RPM
SRP017611_liver	0.00 RPM	16.38 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1813 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1813 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000008036	2 retrocopies	retro_fcat_1813 , retro_fcat_1995,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689,
Ictidomys tridecemlineatus	ENSSTOG00000014871	1 retrocopy	retro_itri_514,