RetrogeneDB ID: retro_fcat_787

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B2:108525127..108525507(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM12
• Ensembl ID: ENSFCAG00000029083
• Aliases: None
• Description: LSM12 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26407]

Sequence

>retro_fcat_787
AATGACTGAACAGAAACCCATCCTCCACTAGCTGCACTCACTGTTAGTAAGCTTACCAGCAAAGCATGGACAGAGAAGGA
GGAGAAGCTGAGCCAGGCTTATGCAATCAGTGCTGGTGTCTCCCTAGAGGGCCAGCAGCTCTTCCAGACCGTACACAAGA
CCTTTAAAGACTGTAAATGGCAAGAAAAAAAACCTCATAGTCATGGAAGAAGTTGTTAACACACCGACCATACCAAGTGG
AAAACTGTAAAAGCAAAGAGAAGCATGCACTGAGCCATGTATGCAAAATGGTTTAAAAACACTTTAGAGACACTGAAAGT
CAAAAGATACTGCCGCGGTCACAAGCCCAGCAACCACAGAAGGAGACTGCCCTGTTATCC

Alignment

ORF - retro_fcat_787 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.69 %
• Parental protein coverage: 64.62 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NDRTETPPPLASLNVSKLASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQ-EKNIVVME
          ND.TET.PPLA.L.VSKL.SKA.TEKEEKLSQAYAISAGVSLEGQQLFQT.HKT.KDCKWQ......VME
Retrocopy ND*TETHPPLAALTVSKLTSKAWTEKEEKLSQAYAISAGVSLEGQQLFQTVHKTFKDCKWQ>XXXLIVME

Parental  EVVITP-PYQVENCKGKEGSALSHVRKIVEKHFRDVESQKILQRSQAQQPQKEAALSS
          EVV.TP.PYQVENCK.KE..ALSHV.K.V.KHFRD.ESQKIL.RSQAQQPQKE.AL.S
Retrocopy EVVNTP>PYQVENCKSKEKHALSHVCKMV*KHFRDTESQKILPRSQAQQPQKETALLS

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	28.46 RPM
SRP017611_kidney	0.00 RPM	25.35 RPM
SRP017611_liver	0.00 RPM	24.26 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_787 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_787 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014379	2 retrocopies	retro_cfam_1843, retro_cfam_312,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Felis catus	ENSFCAG00000029083	1 retrocopy	retro_fcat_787 ,
Homo sapiens	ENSG00000161654	1 retrocopy	retro_hsap_4041,
Loxodonta africana	ENSLAFG00000005202	1 retrocopy	retro_lafr_906,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3,
Mus musculus	ENSMUSG00000020922	1 retrocopy	retro_mmus_2683,
Otolemur garnettii	ENSOGAG00000010489	2 retrocopies	retro_ogar_1771, retro_ogar_2447,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12,
Rattus norvegicus	ENSRNOG00000020894	1 retrocopy	retro_rnor_2845,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062, retro_tbel_60,
Vicugna pacos	ENSVPAG00000011145	1 retrocopy	retro_vpac_627,