RetrogeneDB ID: retro_fcat_1052

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:90540178..90540598(-)
• Located in intron of: ENSFCAG00000023896

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUB1
• Ensembl ID: ENSFCAG00000006012
• Aliases: None
• Description: SUB1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:19985]

Sequence

>retro_fcat_1052
ACTTGCAAGCAAGTGAGCAGAGGGCTGTTCAGCTGCAAGAGTGGAGCAAGCCTAAGTCAAAGGAACTTGTTTCTTCAAGC
TCTTCGGGCAGTGATTCTGAGTGTCAGGTTGACAAAAAGTTAAAGCGGAAAAGGCAGGTTACTCCAGAAAAACCTGTAAA
GAAGCAAAAGACCGGTGAGACTTCAAGAGCCCTATCATCCTCTAAGAAGAGTAGGAGCCACAGAGATGATAACATGTTTC
AGACTGGGAAAATGAGGTATGTCAGTGTTCGAGACTATAAACGGAAAGTCCTAATTGATATTAGAGAATACTGGATGGAT
CAGGAAGGTGAAATAAAACCAGGAAGAAAAGGTATTTCTTTAAATCCTAAGCAAATGGAGCCAGCTGAAGGAACAGATTT
CTGACACTGATGATGCAGTA

Alignment

ORF - retro_fcat_1052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.21 %
• Parental protein coverage: 97.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SCKRASRGLFGCKSGAM-PKSKELVSSSSSGSDSDSEVDKKLKRKKQVTPEKPVKKQKTGETSRALSSSK
          .CK..SRGLF.CKSGA..PKSKELVSSSSSGSDS...VDKKLKRK.QVTPEKPVKKQKTGETSRALSSSK
Retrocopy TCKQVSRGLFSCKSGAS<PKSKELVSSSSSGSDSECQVDKKLKRKRQVTPEKPVKKQKTGETSRALSSSK

Parental  QSSSSRDDNMFQIGKMRYVSVRDFKGKVLIDIREYWMDPEGEMKPGRKGISLNPEQ-WSQLKEQISDIDD
          .S.S.RDDNMFQ.GKMRYVSVRD.K.KVLIDIREYWMD.EGE.KPGRKGISLNP.Q.WSQLKEQISD.DD
Retrocopy KSRSHRDDNMFQTGKMRYVSVRDYKRKVLIDIREYWMDQEGEIKPGRKGISLNPKQ>WSQLKEQISDTDD

Parental  AV
          AV
Retrocopy AV

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	100.43 RPM
SRP017611_kidney	0.00 RPM	61.63 RPM
SRP017611_liver	0.00 RPM	27.70 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1052 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1052 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 17 parental genes, and 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006238	2 retrocopies	retro_amel_1331, retro_amel_794,
Canis familiaris	ENSCAFG00000018879	5 retrocopies	retro_cfam_1266, retro_cfam_1536, retro_cfam_1916, retro_cfam_2010, retro_cfam_215,
Felis catus	ENSFCAG00000006012	2 retrocopies	retro_fcat_1052 , retro_fcat_1313,
Gorilla gorilla	ENSGGOG00000027033	3 retrocopies	retro_ggor_1063, retro_ggor_1254, retro_ggor_2645,
Loxodonta africana	ENSLAFG00000011006	1 retrocopy	retro_lafr_19,
Macropus eugenii	ENSMEUG00000007770	4 retrocopies	retro_meug_1155, retro_meug_1820, retro_meug_2038, retro_meug_500,
Microcebus murinus	ENSMICG00000014535	2 retrocopies	retro_mmur_1115, retro_mmur_17,
Myotis lucifugus	ENSMLUG00000013685	6 retrocopies	retro_mluc_1649, retro_mluc_1696, retro_mluc_1785, retro_mluc_226, retro_mluc_2346, retro_mluc_621,
Monodelphis domestica	ENSMODG00000020410	3 retrocopies	retro_mdom_840, retro_mdom_841, retro_mdom_895,
Mustela putorius furo	ENSMPUG00000015185	2 retrocopies	retro_mputfur_186, retro_mputfur_295,
Mus musculus	ENSMUSG00000022205	4 retrocopies	retro_mmus_1118, retro_mmus_2304, retro_mmus_2586, retro_mmus_3606,
Oryctolagus cuniculus	ENSOCUG00000006262	5 retrocopies	retro_ocun_1227, retro_ocun_1313, retro_ocun_1661, retro_ocun_1714, retro_ocun_902,
Otolemur garnettii	ENSOGAG00000009012	6 retrocopies	retro_ogar_1130, retro_ogar_1272, retro_ogar_218, retro_ogar_2481, retro_ogar_340, retro_ogar_525,
Ochotona princeps	ENSOPRG00000012887	2 retrocopies	retro_opri_495, retro_opri_941,
Pongo abelii	ENSPPYG00000015379	2 retrocopies	retro_pabe_124, retro_pabe_1371,
Rattus norvegicus	ENSRNOG00000050563	12 retrocopies	retro_rnor_1040, retro_rnor_1137, retro_rnor_1203, retro_rnor_1496, retro_rnor_1692, retro_rnor_1693, retro_rnor_1863, retro_rnor_2721, retro_rnor_2986, retro_rnor_420, retro_rnor_572, retro_rnor_735,
Sarcophilus harrisii	ENSSHAG00000014986	1 retrocopy	retro_shar_628,