RetrogeneDB ID: retro_cfam_1940

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 8:10936817..10937344(-)
• Located in intron of: ENSCAFG00000013144

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA3
• Ensembl ID: ENSCAFG00000014650
• Aliases: None
• Description: cell division cycle associated 3 [Source:HGNC Symbol;Acc:14624]

Sequence

>retro_cfam_1940
CCCACAAGCCCTCTGGTAAAATAGCTGAATAAAGTCTGTGAGACAGAAGCCCACAAATCAAATCTTCCCCGAGGGCCTGT
TATAACCTCAGAGGCACCTTCATCTGAATTGGACTTGCCTCCAAACACCCAGTTATTCCAGATGACACACTGAAGCCAGA
CTGAGCTCCCTTCCAAGCAAGCGTTTTCCAAGGAGGAAACAAGACAGCTCACAGAAAGCCCTATGGCCAGCCAGGGCTCA
AACATCTTGAGAGATCTGAGACTCCTCAATCTTCAGGTTCTAAGCGCAACAGAAAGAAATCAAATGGCAAGGTACTAGAG
AGATCTCATTTCACCATCCAGCAAGATGACAATGCCTCTGGAATCCTAACACAAGAGGGTAAGCAGTCTTCTTCCCTAAG
TGGAAATGTTAGGCAACTAAAGGAAGGGGGCATTCTGGGAACTGCACTTCTAAAAACTAGAGGCTGAGCAGAGGAGCAAA
GCTGGGACCATGACAAGAAAAATCAGCACTTTTCCTTGGTAGAAAAC

Alignment

ORF - retro_cfam_1940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.08 %
• Parental protein coverage: 68.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPSPLVKQLSEVFETEAPKSNLPPEPVLPLEATSSSELDLPLGTQFSLEDQMPPWSQTELPSKQVFPKEE
          P.SPLVK.L..V.ETEA.KSNLP..PV...EA.SS.ELDLP..TQ.....QM...SQTELPSKQ.F.KEE
Retrocopy PTSPLVK*LNKVCETEAHKSNLPRGPVITSEAPSS-ELDLPPNTQLF---QMTH*SQTELPSKQAFSKEE

Parental  AGQPSETPMASQGSDKPLRD-PETPRSSGSKHNRRKTNGKALGRSPLTILQDDNSPGTLPPRQGKWPSPL
          ..Q..E.PMASQGS...LRD..ETP.SSGSK.NR.K.NGK.L.RS..TI.QDDN..G.L....GK..S.L
Retrocopy TRQLTESPMASQGSN-ILRD<SETPQSSGSKRNRKKSNGKVLERSHFTIQQDDNASGIL-TQEGKQSSSL

Parental  SENPRELKEGASLGSGRLLKTGGRMWEQDQDQDKENQHFPNLVEN
          S.N.R.LKEG..LG...LLKT.G...EQ..D.DK.NQHF..LVEN
Retrocopy SGNVRQLKEGGILGTA-LLKTRG*AEEQSWDHDKKNQHF-SLVEN

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	4.66 RPM
SRP017611_brain	0.00 RPM	0.64 RPM
SRP017611_kidney	0.00 RPM	0.13 RPM
SRP017611_liver	0.00 RPM	0.36 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1940 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1940 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1940 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013985	1 retrocopy	retro_amel_1158,
Canis familiaris	ENSCAFG00000014650	4 retrocopies	retro_cfam_1100, retro_cfam_1940 , retro_cfam_345, retro_cfam_633,
Cavia porcellus	ENSCPOG00000012334	1 retrocopy	retro_cpor_1073,
Felis catus	ENSFCAG00000004274	2 retrocopies	retro_fcat_1182, retro_fcat_1942,
Mustela putorius furo	ENSMPUG00000016781	1 retrocopy	retro_mputfur_663,
Pteropus vampyrus	ENSPVAG00000012300	4 retrocopies	retro_pvam_235, retro_pvam_248, retro_pvam_297, retro_pvam_667,
Rattus norvegicus	ENSRNOG00000015529	1 retrocopy	retro_rnor_2685,
Ictidomys tridecemlineatus	ENSSTOG00000023573	1 retrocopy	retro_itri_804,
Tupaia belangeri	ENSTBEG00000001905	1 retrocopy	retro_tbel_534,
Vicugna pacos	ENSVPAG00000009784	1 retrocopy	retro_vpac_296,