RetrogeneDB ID: retro_cfam_1309

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:23458856..23460096(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF13
• Ensembl ID: ENSCAFG00000000663
• Aliases: DCAF13, WDSOF1
• Description: DDB1 and CUL4 associated factor 13 [Source:HGNC Symbol;Acc:24535]

Sequence

>retro_cfam_1309
ACCTTACATTCTTTTAAGGTCCCATAAAAATACGTAAGAGCTTTAAACACTCCCAAACTGGAACAGGTATTTGCAAAACC
ATTCCTCGCTTCCCTGGATGGTCACCAAGATGAAGTCAATGCTTGGCAAAGCATCCAAAGAGGCTGGCTACTATCCTTTC
TGGGGCATGTGATGGAGAGGTTAGAATTTGGAACTTGACAAATGAAAATGTATCTGTACAATACAAACACATGAGGGTTT
TATAGAAGGAATATGTACTCTTTTATGTGGGACTTCTTTTATTTTACTGTTGGTGATGACAAAACCGTGAAGTAGTGGAA
AATGAATAGACCAGGTTATGGAAAGGGAGGAACCAGCCATTGCATAAATATTAGAAAAGGGAGTATATACAGGAATTGAT
CATCGCTGAAAGAAGCTGTTTTTGCAACATGTGGACAACAAGTAGACATTTGGGATAAACAAAGAGCCAATCCTACATAT
TCAATGACCTGGGGGTTCGACAGTATAACTAGTGTTAAATTTAATCCAATTGAAACATTTCTCTTGGGGAATAGTACTTC
CAACAGGAATACAGTGCTTTATGATATGAGGTAAGGTATTCCTCTGAAAAAGATCATCTTAGAGATAAGAACGAATATGA
TCTGTTGGAATCCTATGGAAGCTTTAATTCTTACTGCAGCAAATGAAGATTACAACTTATATACTTTTGATATGTATGCA
CTGAACACTCCTGCAGTGGTACATAAGGATCACATATCTGTAGTGCTTGATGTACATTACTCTCCCAATAGGAAAGAGTT
TGTGTCTGCCAGTTTTGATAAATCTATTTGAAACTTTCCTGTGGACAAAAATAGAATCAGGGAAATCTATCACACAAAAA
GAATGCAACATGTTATCTGTGTAAAATGGACTTCTAACAGCAAATATATTACATGTGGATCTGATGAAATGAACATTTGT
CTGTAGAAAGCTAATGGTTCTGAATATTGGGTATGCTTACATAACAAGAAAAAGCAGCCAAGATTACAACCAGAAGTCGA
AAGAGAAATTTCAGCATCATTCGCATATAAAGTGCCTTGCTTGTCACCAATTTCTATCAAAATCTATCTACAGCCATATC
CAGGAACAGCACATCATGAAAGAAGCCTGTCAACGAAAGGAAGTGAATCATCTCAAACACCGCAAGCCTGGATCTGTTCA
GATTGTGTCAGAAAAGAAGTAGTACTTAGTGACAGTTGTG

Alignment

ORF - retro_cfam_1309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.17 %
• Parental protein coverage: 93.03 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  TLHPFEVPREYVRALNATKLERVFAKPFLASLDGHRDGVN-CLAKHPKSLATVLSGACDGEVRIWNLT-K
          TLH.F.VP..YVRALN..KLE.VFAKPFLASLDGH.D.VN.CLAKHPK.LAT.LSGACDGEVRIWNLT.K
Retrocopy TLHSFKVP*KYVRALNTPKLEQVFAKPFLASLDGHQDEVN<CLAKHPKRLATILSGACDGEVRIWNLT<K

Parental  RKCIRTIQAHE-GFVRGICTRFCGTSF-FTVGDDKTVKQWKMDGPGYGE-EEEPLHTILGKTVYTGIDHH
          .KCI.TIQ.HE.GF.R.....F....F.FTVGDDKTVK.WKM..PGYG..EE.....IL.K.VYTGIDH.
Retrocopy *KCICTIQTHE<GFYRRNMYSFMWDFFYFTVGDDKTVK*WKMNRPGYGK>EEPAIA*ILEKGVYTGIDHR

Parental  -WKEAVFATCGQQVDIWDEQRTSPICSMTWGFDSISSVKFNPIETFLLGSCASDRNIVLYDMRQATPLKK
          ..KEAVFATCGQQVDIWD.QR..P..SMTWGFDSI.SVKFNPIETFLLG...S.RN.VLYDMR...PLKK
Retrocopy <LKEAVFATCGQQVDIWDKQRANPTYSMTWGFDSITSVKFNPIETFLLGNSTSNRNTVLYDMR*GIPLKK

Parental  VILDMRTNTICWNPMEAFIFTAANEDYNLYTFDMRALDTPVMVHMDHVSAVLDVDYSPTGKEFVSASFDK
          .IL..RTN.ICWNPMEA.I.TAANEDYNLYTFDM.AL.TP..VH.DH.S.VLDV.YSP..KEFVSASFDK
Retrocopy IILEIRTNMICWNPMEALILTAANEDYNLYTFDMYALNTPAVVHKDHISVVLDVHYSPNRKEFVSASFDK

Parental  SIRIFPVDKSRSREVYHTKRMQHVICVKWTSDSKYIMCGSDEMNIRLWKANASEK-LGVLTSREKAAK-D
          SI..FPVDK.R.RE.YHTKRMQHVICVKWTS.SKYI.CGSDEMNI.L.KAN.SE..LG.LT..EKAAK.D
Retrocopy SI*NFPVDKNRIREIYHTKRMQHVICVKWTSNSKYITCGSDEMNICL*KANGSEY<LGMLT*QEKAAK<D

Parental  YNQKLKEKFQHHPHIKRIARHRHLPKSIYSQIQEQRIMKEARRRKEVNRLKHSKPGSVSIVPEKKKHIVA
          YNQK.KEKFQHH.HIK..A.H..L.KSIYS.IQEQ.IMKEA..RKEVN.LKH.KPGSV.IV.EKK...V.
Retrocopy YNQKSKEKFQHHSHIKCLACHQFLSKSIYSHIQEQHIMKEACQRKEVNHLKHRKPGSVQIVSEKK*YLVT

Parental  VV
          VV
Retrocopy VV

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
SRP012049_cerebellum	0.00 RPM	13.15 RPM
SRP017611_brain	0.00 RPM	9.13 RPM
SRP017611_kidney	0.00 RPM	24.90 RPM
SRP017611_liver	0.00 RPM	6.24 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1309 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1309 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1309 has 0 orthologous retrocopies within eutheria group .

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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,