RetrogeneDB ID: retro_fcat_1885

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: JH408894.1:15274..15688(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSFCAG00000012352
• Aliases: None
• Description: small nuclear ribonucleoprotein D1 polypeptide 16kDa [Source:HGNC Symbol;Acc:11158]

Sequence

>retro_fcat_1885
ACTTGGGTGGTTGCGTTTTGTGCGCTACCCGACTGAAAGAGTGCCGGCACCACTAGGATGAAGCTCATAAGATTTTTGAT
GAAATTGAGTTATGAGACCGTAACCATTGAAGTAAAGAATGGAACACAGGTCCATGGAACAATCACAGATGTAGATGTCA
GAATGAATACACATCTTAAAGCAGTGAAAATGACTTTGAAGGATAGAGAACCAGTATAATTGGAAACACTGAGTATTCGA
GGAAATAACATTTGATATTTTATACTGCCAGACAGCTTACCTCTGGATACACTACTTCTGGATGTTGAACCGAAGGTGAA
ATCTAAGAAAAGGGAAGCTGTTGCAGGAAGAGGCTGAGGCCGAGGAAGAGGAAGAGGACGTGGTTGGGGTAGAGGAAGAG
GGGGTCCTAGGCGA

Alignment

ORF - retro_fcat_1885 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.86 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TWVVAFCALSDRKSAGTARMKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNRE
          TWVVAFCAL.D.KSAGT.RMKL.RFLMKLS.ETVTIE.KNGTQVHGTIT.VDV.MNTHLKAVKMTLK.RE
Retrocopy TWVVAFCALPD*KSAGTTRMKLIRFLMKLSYETVTIEVKNGTQVHGTITDVDVRMNTHLKAVKMTLKDRE

Parental  PVQLETLSIRGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR
          PV.LETLSIRGNNI.YFILPDSLPLDTLL.DVEPKVKSKKREAVAGRG.GRGRGRGRG.GRGRGGPRR
Retrocopy PV*LETLSIRGNNI*YFILPDSLPLDTLLLDVEPKVKSKKREAVAGRG*GRGRGRGRGWGRGRGGPRR

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	1.95 RPM	8.84 RPM
SRP017611_kidney	0.21 RPM	10.72 RPM
SRP017611_liver	0.00 RPM	5.46 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1885 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1885 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006364	1 retrocopy	retro_acar_129,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Canis familiaris	ENSCAFG00000018247	1 retrocopy	retro_cfam_373,
Dasypus novemcinctus	ENSDNOG00000018773	4 retrocopies	retro_dnov_1254, retro_dnov_1716, retro_dnov_1832, retro_dnov_2403,
Felis catus	ENSFCAG00000012352	1 retrocopy	retro_fcat_1885 ,
Macaca mulatta	ENSMMUG00000003992	2 retrocopies	retro_mmul_887, retro_mmul_891,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Pongo abelii	ENSPPYG00000025874	3 retrocopies	retro_pabe_254, retro_pabe_948, retro_pabe_952,
Pan troglodytes	ENSPTRG00000009909	2 retrocopies	retro_ptro_291, retro_ptro_781,
Pteropus vampyrus	ENSPVAG00000005511	1 retrocopy	retro_pvam_450,
Rattus norvegicus	ENSRNOG00000013714	2 retrocopies	retro_rnor_2671, retro_rnor_2729,
Tursiops truncatus	ENSTTRG00000002654	2 retrocopies	retro_ttru_1566, retro_ttru_1890,