RetrogeneDB ID: retro_fcat_1134

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: C1:149738055..149739299(+)
• Located in intron of: ENSFCAG00000023012

Retrocopy information

• Ensembl ID: ENSFCAG00000023570
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: OSBPL9
• Ensembl ID: ENSFCAG00000010298
• Aliases: None
• Description: oxysterol binding protein-like 9 [Source:HGNC Symbol;Acc:16386]

Sequence

>retro_fcat_1134
AGTACTATTAATCCTGTAGATGCAATATATCAACCTAGTCCCTTGGAACCTGTGATCAAAACAATGCCTACTCAGACTGT
CTTGCCTCCAGAACCTGCTCAGTTGTGTAAGTCAGGGCAGCATCCATCTTCCCTACCAGTTTGACCTGTATTAGCTACCT
TGGGACATCATCAGACTCCAACACCAAATAGTACAGGCAGTGGGCACTCACCACCTAGTAGCAGTTTGACTTCTCCAAGC
CATGTCAACTTGTCTCCAAATACTGTCCCTGAGTTCTCTTATTCTAGCAGCAAAGATGAATTCTATGATGCTGATGAATT
TCATCAAAGTGGCTCATCCCCAAAGCACTTAATAGATTCCTGTGGATCTGCCTCTGTCTTGACAAACAGCAGCTCAGGAA
ATAGTCGCAAGCGCCCCGATACCACAGAGTCACTTAATTCTTCCATGTCCAATGGAACAAGCGATGCTGACCTCTTTGAT
TCACATGAGGATAGAGATGATGAAGGGGAGGCAGGGTCCATGGAAGAGCACAAGAGCGTTGTCATGCATCTCTTGTCACA
GGTTAGGCTTGGAATGGATCTTACTAAGGTAGTTCTTCCAACATTATTCTTGAAAGAAGATCTCTGTTAGAAATGTATGC
AGACTTTTTTGCACATCTGGACCTGTTTGTGAGCATTAGTGACCAGAAGGATGCCAGAGATCGAATGGTTCAGGTTGTGA
AATGGTACCTCTCAGCCTTTCACGCAGGAAGGAAAGGATTGGTTGCCAAAAAGCCATACAACCCTATTTTGGGTGAAATC
TTTCAGTGTCACTGGACATTACCAAATGATACTGAAGAGAACCCAGAACTAGTTTCAGAAGGACCAGTTCCCTGGGTTTC
CAAAAACTGTGACATTCATGGCTGAGCAGGTTTCCCATCATCCACCCATTTCAGCTTTTTATGCTGAGCGTTTTAACAAA
AAGATACAATTCAATGCTCATATCTGGACCAAATCAAAATTCCTTGGGATGTCGATTGGGGTGCACAACATAGGGCAGGG
CTGTGTCTCATGTCTAGATTATGACGAACATTACATTCTCACATTCCCCAATGGTTATGGAAGGTCTGTCCTCACAGTGC
CCTGGGTGGAACTAGGTAGAGAATGCAATATCAATTGTTCCAAAACTGGCTATAGTGCAAATATCGTCTTCCACACTAAA
CCTTTCTGTGGGGCAAGAAGCACAGAATTACTGCTGAGATTTTG

Alignment

ORF - retro_fcat_1134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.08 %
• Parental protein coverage: 64.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  STINPVDAIYQPSPLEPVINTMPTQTVLPPEPAQLCKSEQRPSSLPVGPVLATLGHHQTPTPNSTGSGHS
          STINPVDAIYQPSPLEPVI.TMPTQTVLPPEPAQLCKS.Q.PSSLPV.PVLATLGHHQTPTPNSTGSGHS
Retrocopy STINPVDAIYQPSPLEPVIKTMPTQTVLPPEPAQLCKSGQHPSSLPV*PVLATLGHHQTPTPNSTGSGHS

Parental  PPSSSLTSPSHVNLSPNTVPEFSYSSSEDEFYDADEFHQSGSSPKRLIDSSGSASVLTHSSSGNSLKRPD
          PPSSSLTSPSHVNLSPNTVPEFSYSSS.DEFYDADEFHQSGSSPK.LIDS.GSASVLT.SSSGNS.KRPD
Retrocopy PPSSSLTSPSHVNLSPNTVPEFSYSSSKDEFYDADEFHQSGSSPKHLIDSCGSASVLTNSSSGNSRKRPD

Parental  TTESLNSSMSNGTSDADLFDSHDDRDDEGEAGSVEEHKSVIMHLLSQVRLGMDLTKVVLPTF-ILERRSL
          TTESLNSSMSNGTSDADLFDSH.DRDDEGEAGS.EEHKSV.MHLLSQVRLGMDLTKVVLPT..ILERRSL
Retrocopy TTESLNSSMSNGTSDADLFDSHEDRDDEGEAGSMEEHKSVVMHLLSQVRLGMDLTKVVLPTL<ILERRSL

Parental  LEMYADFFAHPDLFVSISDQKDARDRMVQVVKWYLSAFHAGRKGSVAKKPYNPILGEIFQCHWTLPNDTE
          LEMYADFFAH.DLFVSISDQKDARDRMVQVVKWYLSAFHAGRKG.VAKKPYNPILGEIFQCHWTLPNDTE
Retrocopy LEMYADFFAHLDLFVSISDQKDARDRMVQVVKWYLSAFHAGRKGLVAKKPYNPILGEIFQCHWTLPNDTE

Parental  ENAELVSEGPV-PWVSKNCVTFVAEQVSHHPPISAFYAECFNKKIQFNAHIWTKSKFLGMSIGVHNIGQG
          EN.ELVSEGPV.P...K..VTF.AEQVSHHPPISAFYAE.FNKKIQFNAHIWTKSKFLGMSIGVHNIGQG
Retrocopy ENPELVSEGPV>PGFPKT-VTFMAEQVSHHPPISAFYAERFNKKIQFNAHIWTKSKFLGMSIGVHNIGQG

Parental  CVSCLDYDEHYILTFPNGYGRSILTVPWVELGGECNINCSKTGYSANIVFHTKPFYG-GKKHRITAEIL
          CVSCLDYDEHYILTFPNGYGRS.LTVPWVELG.ECNINCSKTGYSANIVFHTKPF.G.GKKHRITAEIL
Retrocopy CVSCLDYDEHYILTFPNGYGRSVLTVPWVELGRECNINCSKTGYSANIVFHTKPFCG<GKKHRITAEIL

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	0.92 RPM	31.45 RPM
SRP017611_kidney	1.86 RPM	48.13 RPM
SRP017611_liver	1.31 RPM	22.95 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1134 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1134 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021574	1 retrocopy	retro_cjac_1235,
Felis catus	ENSFCAG00000010298	1 retrocopy	retro_fcat_1134 ,
Gorilla gorilla	ENSGGOG00000004787	1 retrocopy	retro_ggor_737,
Microcebus murinus	ENSMICG00000002731	1 retrocopy	retro_mmur_1035,
Myotis lucifugus	ENSMLUG00000009199	1 retrocopy	retro_mluc_2149,
Nomascus leucogenys	ENSNLEG00000016138	2 retrocopies	retro_nleu_1820, retro_nleu_279,
Oryctolagus cuniculus	ENSOCUG00000004303	1 retrocopy	retro_ocun_281,
Pongo abelii	ENSPPYG00000001358	2 retrocopies	retro_pabe_689, retro_pabe_787,
Pan troglodytes	ENSPTRG00000000730	1 retrocopy	retro_ptro_632,
Ictidomys tridecemlineatus	ENSSTOG00000000692	1 retrocopy	retro_itri_1537,