RetrogeneDB ID: retro_fcat_1763

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F1:67254074..67254678(+)
• Located in intron of: ENSFCAG00000012088

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000026474
• Aliases: None
• Description: None

Sequence

>retro_fcat_1763
CAAAGCTTGCTTGAGTTCCTGAATGATGTGAATAAGGAGGAAAAGAAGATCTAGAAGCATAGGTCCCTCCCCAAGATGTC
TGGGGCCTGGGAGCTGGAAGTGGATGGGATAGAAACCAAATTAGTGTGGAAAGTTTCCGGAGAAAAGATGACTGTGACTT
TCAACATGAACAACAGCATCCCAGCAACATTTGATGGGGGAAGAGCCCTCCCAAGGGCAGAAGGTGGAAGAACAGGAGCC
TGAACTGATGTCCATTCCCAGTTTTGTGGTGGAAGGTAAGAATGGTGGCAAGAAGGGCCTGGTACTGGGCTGTCCCTACC
CAGAAGATGAGGTGGGCAAGAAGAGGAGGACGGCAGTGACATTTGGCCGTCAGAGAGGTGAGCGGACAACATCAGTCCGT
TGTCGAGTCTGAGTGAAAGGACACAAGTTACATGCTCACCACCGACTCCCTGGCCTGGACCGTTATGACACCAGCTGGAT
CTTCTGGCCAACCAGGGTTTGGGGGGAGGGCAGTTGGACAACACTTTTGCAGGTGAGCACAGCCCTCGAGCACCAGGAAT
ACGTTACTTTCCTCAAAGATCTGAAAGGTTTTGTCAAGAGCCAG

Alignment

ORF - retro_fcat_1763 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.1 %
• Parental protein coverage: 95.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KAFVEFLNDEIKEEKKIQKHGSLPKMSGGWELEVNGTEATLVRKVAGEKITVTFNINNSIPPTF-AGEEE
          ....EFLND..KEEKKI.KH.SLPKMSG.WELEV.G.E..LV.KV.GEK.TVTFN.NNSIP.TF..GEE.
Retrocopy QSLLEFLNDVNKEEKKI*KHRSLPKMSGAWELEVDGIETKLVWKVSGEKMTVTFNMNNSIPATF>MGEE-

Parental  PSQGQKAEEQEPELTSTPNFVVEVIKNGGKKALVLDCHYPEDEV-GQEEEDESDIF-AIREVS--FQSVG
          PSQGQK.EEQEPEL.S.P.FVVE..KNGGKK.LVL.C.YPEDEV.GQEEED.SDI..A.REVS...QSV.
Retrocopy PSQGQKVEEQEPELMSIPSFVVEG-KNGGKKGLVLGCPYPEDEV<GQEEEDGSDIW<AVREVSGQHQSVV

Parental  ESEWKDTNYTLNTDSLDWAL-YD-HLMDFLADRGVDNTFADE-LVELSTALEHREYITFLEDLKGFVKSQ
          ESE.KDT.Y.L.TDSL.W...YD.H..D.LA..G......D..L...STALEH.EY.TFL.DLKGFVKSQ
Retrocopy ESE*KDTSYMLTTDSLAWTV<YD<HQLDLLANQGLGGGQLDN>LLQVSTALEHQEYVTFLKDLKGFVKSQ

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	29.04 RPM
SRP017611_kidney	0.00 RPM	50.40 RPM
SRP017611_liver	0.10 RPM	34.98 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1763 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1763 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 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006043	2 retrocopies	retro_amel_1734, retro_amel_356,
Canis familiaris	ENSCAFG00000015542	3 retrocopies	retro_cfam_1595, retro_cfam_319, retro_cfam_325,
Callithrix jacchus	ENSCJAG00000011352	6 retrocopies	retro_cjac_2041, retro_cjac_2408, retro_cjac_4033, retro_cjac_604, retro_cjac_680, retro_cjac_946,
Dasypus novemcinctus	ENSDNOG00000008887	3 retrocopies	retro_dnov_1151, retro_dnov_1946, retro_dnov_702,
Felis catus	ENSFCAG00000026474	3 retrocopies	retro_fcat_1135, retro_fcat_1763 , retro_fcat_892,
Homo sapiens	ENSG00000108561	2 retrocopies	retro_hsap_1475, retro_hsap_2516,
Gorilla gorilla	ENSGGOG00000002745	5 retrocopies	retro_ggor_1133, retro_ggor_1569, retro_ggor_3007, retro_ggor_3008, retro_ggor_717,
Macropus eugenii	ENSMEUG00000014882	13 retrocopies	retro_meug_1068, retro_meug_1347, retro_meug_1363, retro_meug_1446, retro_meug_1901, retro_meug_1940, retro_meug_1970, retro_meug_2069, retro_meug_2128, retro_meug_434, retro_meug_580, retro_meug_988, retro_meug_989,
Macaca mulatta	ENSMMUG00000006592	1 retrocopy	retro_mmul_1554,
Mustela putorius furo	ENSMPUG00000011246	1 retrocopy	retro_mputfur_1213,
Nomascus leucogenys	ENSNLEG00000009081	2 retrocopies	retro_nleu_2379, retro_nleu_3038,
Otolemur garnettii	ENSOGAG00000001610	5 retrocopies	retro_ogar_1376, retro_ogar_2502, retro_ogar_2518, retro_ogar_2879, retro_ogar_768,
Ochotona princeps	ENSOPRG00000013150	1 retrocopy	retro_opri_408,
Pongo abelii	ENSPPYG00000007870	6 retrocopies	retro_pabe_1222, retro_pabe_1385, retro_pabe_1413, retro_pabe_1866, retro_pabe_1868, retro_pabe_670,
Pan troglodytes	ENSPTRG00000008631	3 retrocopies	retro_ptro_1140, retro_ptro_1461, retro_ptro_998,
Pteropus vampyrus	ENSPVAG00000002466	1 retrocopy	retro_pvam_384,
Sarcophilus harrisii	ENSSHAG00000002441	2 retrocopies	retro_shar_620, retro_shar_813,