RetrogeneDB ID: retro_fcat_1840

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: F2:24256346..24257483(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF13
• Ensembl ID: ENSFCAG00000027256
• Aliases: None
• Description: DDB1 and CUL4 associated factor 13 [Source:HGNC Symbol;Acc:24535]

Sequence

>retro_fcat_1840
TACAGAGATAAAGTCAATTGTTTGGCAAAGCATCCAAAGAGCCTGGCTACTGTCCTTCCTGGGGCATGTGATTGAGAGAT
TAGAATTTGGAACTCAACTAAATGAAAAAGTATCCATACAATACAAGCACATGAGAGTTTTGTATAAGGAATACATACTT
GTTTTTGTGGGACTTTTTTTTTTAACTGTTGGTGATGACAAAACTGTGAAGCAGTAGAAAATGGATGGACTGGGCTACGG
AGAAGAGGAGGAACCACTGCATACGACATTAGGAAAGAGAGTGTATACAGGAATTGCTCATCACTGGAAAGAAGCTGTTT
TTGCCACATGTGGACACCAAGTAGACATTTGGGATGAACAAAGAACCAATCCTATATGTTCGATGATCTAGGGATTTGAC
AGTAGTGTTAAACTTAATCCAACTGACACATTTCTCTTGGGCAGTTGTGCTTCTGACAGGAATATAGTACTATATGATAT
GAGGCAAGATACTCCTCTGAAAAATGTCATCTTAGGTATGGGAACAAATACAATTTGTTGGAACCCTATGGAAGCTTTCA
TTTTTACTGCAGCAAATGAAGATTACAACTTCTATGCATTTCAGAAGCATCCACTATACACTCTTGTAATGGTATGTGTG
GATCTGTATCTGCAGTGCTTAATGTACATTATTCTCCCACTGGGAAAGACTTGATGTCTGCTAGTTTTGATGAATCGATT
TGAATCTTTCCTATTGGCAAAAAAAGAAATGGGTTAGTCTATCATGCAAAGAGAATGCAACATGTTCTCTGTATAAAATA
GACTTCTAACAGCAAATATATTACGTGTGGATCTGATGAAATGGACATTTGTCTGTGGAAGGCTAATGCTTCTGAAAAAC
TGGATGTGCTTACTTCACGAGAAGAAGCAGCCAAAGGGTATAGCCAGAAGTTGAAGGAGAAACTTCAACACCATCTTCAT
ATAAAACGCGTTGCTCATCACCGATATCTACCAAAATCTATCTACACCCAGATTCAAGAACAGCACACCATTAAAGAAGT
TGGTCAACAAAAGGAAGGGAATCGTTTTAAACACAGCAAGCCTGGATCTGTACTGATTGTGTCAGACAAGAAGGAATACA
TAGTGACAGTTCTGAAA

Alignment

ORF - retro_fcat_1840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.46 %
• Parental protein coverage: 85.62 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HRDGVNCLAKHPKSLATVLSGACDGEVRIWNLTKRKCIRTIQAHEGFVRGICTRFCGTSFF-TVGDDKTV
          .RD.VNCLAKHPKSLATVL.GACD.E.RIWN.TK.K.I.TIQAHE.FV.GI.T.FCG.....TVGDDKTV
Retrocopy YRDKVNCLAKHPKSLATVLPGACD*EIRIWNSTK*KSIHTIQAHESFV*GIHTCFCGXXXX>TVGDDKTV

Parental  KQWKMDGPGYGEEEEPLHTILGKTVYTGIDHHWKEAVFATCGQQVDIWDEQRTSPICSMTWGFDSISSVK
          KQ.KMDG.GYGEEEEPLHT.LGK.VYTGI.HHWKEAVFATCG.QVDIWDEQRT.PICSM..GFDS..SVK
Retrocopy KQ*KMDGLGYGEEEEPLHTTLGKRVYTGIAHHWKEAVFATCGHQVDIWDEQRTNPICSMI*GFDS--SVK

Parental  FNPIETFLLGSCASDRNIVLYDMRQATPLKKVILDMRTNTICWNPMEAFIFTAANEDYNLYTFDMRALDT
          .NP..TFLLGSCASDRNIVLYDMRQ.TPLK.VIL.M.TNTICWNPMEAFIFTAANEDYN.Y.F....L.T
Retrocopy LNPTDTFLLGSCASDRNIVLYDMRQDTPLKNVILGMGTNTICWNPMEAFIFTAANEDYNFYAFQKHPLYT

Parental  PVMVHMD-HVSAVLDVDYSPTGKEFVSASFDKSIRIFPVDKSRSREVYHTKRMQHVICVKWTSDSKYIMC
          .VMV..D..VSAVL.V.YSPTGK...SASFD.SI.IFP..K.R...VYH.KRMQHV.C.K.TS.SKYI.C
Retrocopy LVMVCVD<SVSAVLNVHYSPTGKDLMSASFDESI*IFPIGKKRNGLVYHAKRMQHVLCIK*TSNSKYITC

Parental  GSDEMNIRLWKANASEKLGVLTSREKAAKDYNQKLKEKFQHHPHIKRIARHRHLPKSIYSQIQEQRIMKE
          GSDEM.I.LWKANASEKL.VLTSRE.AAK.Y.QKLKEK.QHH.HIKR.A.HR.LPKSIY.QIQEQ...KE
Retrocopy GSDEMDICLWKANASEKLDVLTSREEAAKGYSQKLKEKLQHHLHIKRVAHHRYLPKSIYTQIQEQHTIKE

Parental  ARRRKEVNRLKHSKPGSVSIVSEKKKHIVAVVK
          ....KE.NR.KHSKPGSV.IVS.KK..IV.V.K
Retrocopy VGQQKEGNRFKHSKPGSVLIVSDKKEYIVTVLK

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	14.35 RPM
SRP017611_kidney	0.00 RPM	26.69 RPM
SRP017611_liver	0.00 RPM	9.10 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_1840 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_1840 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001595	3 retrocopies	retro_amel_1453, retro_amel_1723, retro_amel_399,
Canis familiaris	ENSCAFG00000000663	3 retrocopies	retro_cfam_1309, retro_cfam_1533, retro_cfam_305,
Callithrix jacchus	ENSCJAG00000016181	2 retrocopies	retro_cjac_3083, retro_cjac_612,
Felis catus	ENSFCAG00000027256	1 retrocopy	retro_fcat_1840 ,
Homo sapiens	ENSG00000164934	1 retrocopy	retro_hsap_1498,
Gorilla gorilla	ENSGGOG00000015124	1 retrocopy	retro_ggor_1150,
Myotis lucifugus	ENSMLUG00000007375	1 retrocopy	retro_mluc_2048,
Nomascus leucogenys	ENSNLEG00000003791	1 retrocopy	retro_nleu_1718,
Otolemur garnettii	ENSOGAG00000002277	1 retrocopy	retro_ogar_305,
Pongo abelii	ENSPPYG00000018809	2 retrocopies	retro_pabe_1249, retro_pabe_3211,
Pan troglodytes	ENSPTRG00000020493	1 retrocopy	retro_ptro_1017,
Sarcophilus harrisii	ENSSHAG00000006588	1 retrocopy	retro_shar_507,