RetrogeneDB ID: retro_cfam_223

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:22924485..22926180(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000013603
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000031010
• Aliases: DCAF8, WDR42A
• Description: None

Sequence

>retro_cfam_223
GGGAGAGAGACATCTTCAGACACGGAGCTGAGCTTGAATTTGCCCGGAGATGGCGGCATCCTCAGCCAGGTCGGCCCAGA
AGACGAAGGCACAGACGCAGACGTTTCGAGTGAATACATCAACTTTGAAGGCACGCAAGATTCTGACCAATTCTTCGTCT
GTGAGGAAAACCTGTCCCCTTACCGCCCAGAAGGAGAGGAGGCGCGAGGCGCGGAAGCGGAGGAGAGAGGAGCGGCAGAA
GAACAGCCGCAGGTACAGTGCAATGAGGCTAATTATGATCAGTATTTATCAGATGAGGATCGGGCCCTGGAGGAGTGGGT
GACCTCCGAAACATCTACCCTGCCCCGCCCTCGCTGGCAAATCGTTTCCGCTCTTCGAGAGCGGCAGCTGGGTTCCAGTG
CCCGCTTCGTATATGAGGCCTGTGGGGCAAGGCTGTTTGTGCAGCGTTTCCACCTGCTCCATGAGCTTGAAGGCCACCAT
GGTTGTGTCAATACTGTGCACTTTAATCAGCGTGGCACCTGGCTGGCCAGTAGCAGCGACGACCTTAAAGTGATAGTGTG
GGACTGGGTGCGTAAGCACCCAGTACTGGAGTTTATGAGTGGCCACAAAAATAATGTCTTTCAAGCCAAGTTCCTTCCCA
ATTGTGGTGATTCCACCTTGGCGATGTGTGCCCGTGATGGGCAGGTACGCATAGCGGAGCTATCTGCTATACCACACTGT
AAGAATACTAAGCGCGTGGCCCAGCATAGGGGAGCCTCCCACAAGCTGGCTCTGGAGCCAGACTCCCCTTTTAAGTTCCT
AACTTCGGGCGAAGACGCAGTTGTTTTCGCCATTGACCTCAGACAAGGCCGGCCAGCTTCCAGAGTGGTGGTAACCAAAG
AGAGGGAGAAGAAAGTGGGGCTGTATACAATCCATGTGAATCCTGCCAATACTTACCAGTTTGCAGTGGGAGGAAGAGAT
CAGTTCGTAAGAATTTATGACCAGAGGAAGATTGATGAGAATGAGAATAATGGGGTACTCAAAAAATTCTGTCCCCATCA
CCTAGTCAATTGTGAGTCCAAAGCAAACATCACCTGCCTGGTGTACAGCCATGATGGCACAGAGCTCCTGGCCAGTTATA
ATGATGAAGATATTTATCTCTTCAACTCCTCTGATGGAGATGGAGCCCAGTATGTTAAGAAATACAAGGGGCACAGAAAT
AATGCCACGATCAAAGGCGTCAATTTCTATGGCCCCAGAAGTGAGTTTGTGGTGAGTGGCAGTGATTGTGGCCACATCTT
CCTCTGGGAAAAATCATCCTGCCAGATCGTTCAGTTCATGGAGGGGGACAAGGGAGGCACCATAAACTGTCTTGAACCCC
ATCCTTACCTACCTGTGATGGCGACCAGTGGCCTTGATCATAATGCCAAGATCTGGGCACCCACAGCTGAAGCTACCACT
GAGCTGACTGGGTTAAAGAATATGATTAAGAGAAACAAGCAAGAACGGGATGAAGATCGCATGCACCACACCGACCTTTT
TGACAGCCACATGCTTTGGTTCCTGATGCGTCACCTAACACAGAGAGGTCATCACCAGCGCCAGAGAGCTCCTGGAGTTG
GAGTCATGGATGCAGAGTCCGATGAGTCTTCCACTACTTCCAGTTCATCTGAGGAGGAAGAGAACCAAGACCATGTGCAG
TGCCTACCGTCCTGA

Alignment

ORF - retro_cfam_223 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.21 %
• Parental protein coverage: 83.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEEEEEEEEHPRRRVQRKRANRDQDSSDDERALEDWVSSETSALPRPRWQALPALRERELGSSARFVYE
          E.EE....EE.P...VQ...AN.DQ..SD..RALE.WV.SETS.LPRPRWQ...ALRER.LGSSARFVYE
Retrocopy EAEERGAAEEQPQ--VQCNEANYDQYLSDEDRALEEWVTSETSTLPRPRWQIVSALRERQLGSSARFVYE

Parental  ACGARVFVQRFRLQHGLEGHTGCVNTLHFNQRGTWLASGSDDLKVVVWDWVRRQPVLDFESGHKSNVFQA
          ACGAR.FVQRF.L.H.LEGH.GCVNT.HFNQRGTWLAS.SDDLKV.VWDWVR..PVL.F.SGHK.NVFQA
Retrocopy ACGARLFVQRFHLLHELEGHHGCVNTVHFNQRGTWLASSSDDLKVIVWDWVRKHPVLEFMSGHKNNVFQA

Parental  KFLPNSGDSTLAMCARDGQVRVAELSATQCCKNTKRVAQHKGASHKLALEPDSPCTFLSAGEDAVVFTID
          KFLPN.GDSTLAMCARDGQVR.AELSA...CKNTKRVAQH.GASHKLALEPDSP..FL..GEDAVVF.ID
Retrocopy KFLPNCGDSTLAMCARDGQVRIAELSAIPHCKNTKRVAQHRGASHKLALEPDSPFKFLTSGEDAVVFAID

Parental  LRQDRPASKLVVTKEKEKKVGLYTIYVNPANTHQFAVGGRDQFVRIYDQRKIDENENNGVLKKFCPHHLV
          LRQ.RPAS..VVTKE.EKKVGLYTI.VNPANT.QFAVGGRDQFVRIYDQRKIDENENNGVLKKFCPHHLV
Retrocopy LRQGRPASRVVVTKEREKKVGLYTIHVNPANTYQFAVGGRDQFVRIYDQRKIDENENNGVLKKFCPHHLV

Parental  NSESKANITCLVYSHDGTELLASYNDEDIYLFNSSHSDGAQYVKRYKGHRNNATVKGVNFYGPKSEFVVS
          N.ESKANITCLVYSHDGTELLASYNDEDIYLFNSS..DGAQYVK.YKGHRNNAT.KGVNFYGP.SEFVVS
Retrocopy NCESKANITCLVYSHDGTELLASYNDEDIYLFNSSDGDGAQYVKKYKGHRNNATIKGVNFYGPRSEFVVS

Parental  GSDCGHIFLWEKSSCQIVQFMEGDKGGVVNCLEPHPHLPVLATSGLDHDVKIWAPTAETSTELTGLKDVI
          GSDCGHIFLWEKSSCQIVQFMEGDKGG..NCLEPHP.LPV.ATSGLDH..KIWAPTAE..TELTGLK..I
Retrocopy GSDCGHIFLWEKSSCQIVQFMEGDKGGTINCLEPHPYLPVMATSGLDHNAKIWAPTAEATTELTGLKNMI

Parental  KKNKRERDEDSLHHTDLFDSHMLWFLMHHLRQRRHHRRWREPGVGATDADSDESPSSSDTSDEEEGPDRV
          K.NK.ERDED..HHTDLFDSHMLWFLM.HL.QR.HH.R.R.PGVG..DA.SDES...S..S.EEE..D.V
Retrocopy KRNKQERDEDRMHHTDLFDSHMLWFLMRHLTQRGHHQRQRAPGVGVMDAESDESSTTSSSSEEEENQDHV

Parental  QCMPS
          QC.PS
Retrocopy QCLPS

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	0.17 RPM	95.46 RPM
SRP017611_brain	0.08 RPM	92.73 RPM
SRP017611_kidney	0.00 RPM	98.40 RPM
SRP017611_liver	0.00 RPM	54.17 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cfam_223 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DN342742	22925058	22925554	99.6	494	2	492

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_223 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Bos taurus	retro_btau_1853
Mus musculus	retro_mmus_111

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014293	1 retrocopy	retro_amel_47,
Bos taurus	ENSBTAG00000005796	1 retrocopy	retro_btau_1853,
Canis familiaris	ENSCAFG00000031010	1 retrocopy	retro_cfam_223 ,
Callithrix jacchus	ENSCJAG00000005913	1 retrocopy	retro_cjac_1322,
Echinops telfairi	ENSETEG00000012876	1 retrocopy	retro_etel_654,
Felis catus	ENSFCAG00000003925	1 retrocopy	retro_fcat_14,
Mustela putorius furo	ENSMPUG00000013949	1 retrocopy	retro_mputfur_173,
Mus musculus	ENSMUSG00000026554	1 retrocopy	retro_mmus_111,
Otolemur garnettii	ENSOGAG00000011349	1 retrocopy	retro_ogar_2113,
Pteropus vampyrus	ENSPVAG00000007982	1 retrocopy	retro_pvam_1356,
Sus scrofa	ENSSSCG00000006388	1 retrocopy	retro_sscr_88,
Tupaia belangeri	ENSTBEG00000001566	1 retrocopy	retro_tbel_3644,