RetrogeneDB ID: retro_cfam_1250

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 27:42988932..42989482(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000003238
• Aliases: None
• Description: None

Sequence

>retro_cfam_1250
AAACTGCAAAGTAAACTCAAACACAGCACTTCTGAATACAGCCCAATGGAAATATACAAGAGGGAATTCTAACTAAAGCT
TGTTGGGAGTATAGCCCAGCCCACGTGGACACTGTCTCTGTTGTTGCTGCTCTGAACTCAGACCTGTGTGTCTCCAGAGG
AAAAGATAAGACAGTTGTGGCCAAAACTGGAAAATCGGAAATGTGATCAAAGGCTCAGAGGACATTAATGAAAGAAATCA
CTAAGGTAGCCTGTATTCACAAATCAAGCCAGTTCTTCAGCATCTGTTGTGACAGGATGGTCATGATGTGGAACTTGTGT
GGTCTTTCACAACCAAGGCAACAGTTTTCCGTAATGCCACGGTGGTCACTGGATTGGCTGTGAGTCCAGGCGTGTCACAC
CTGGGCCCTGGCTTTTGGGACAACACCCTGCTTCTGTGGGATGTTGGGACGGGACGGTGCACAGAGAGAGCCTCCATTTC
CAGGAACCTGCTCACTTACCTGTGCTGGGTCCCCTAAGAACCACAGACTTCTAAGGATAAAACCATCAGA

Alignment

ORF - retro_cfam_1250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.88 %
• Parental protein coverage: 87.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KLQSKLKHSTYKYSRPDEI-IEERTQTKACLEYSPAHVDTVSVVAALNSDLCVSGGRDKTVVA-YNWKTG
          KLQSKLKHST..YS.P.EI.I.E...TKAC.EYSPAHVDTVSVVAALNSDLCVS.G.DKTVVA..NWK.G
Retrocopy KLQSKLKHSTSEYS-PMEI<IQEGILTKACWEYSPAHVDTVSVVAALNSDLCVSRGKDKTVVA<QNWKIG

Parental  NVV-KRFKGHEREITKIACIHKSSQFFSASRDRMVMMWDLHDPSQPRQQFS-GHAMVVTGLAVSPDSSQL
          NV..K.......EITK.ACIHKSSQFFS...DRMVMMW.L...SQPRQQFS...A.VVTGLAVSP..S.L
Retrocopy NVI>KAQRTLMKEITKVACIHKSSQFFSICCDRMVMMWNLCGLSQPRQQFS<RNATVVTGLAVSPGVSHL

Parental  CTGSRDNTLLLWDVGTGQCAERASVSRNLVTHMCWVPQEPYILQTSEDKTIR
          ..G..DNTLLLWDVGTG.C.ERAS.SRNL.T..CWVP.EP...QTS.DKTIR
Retrocopy GPGFWDNTLLLWDVGTGRCTERASISRNLLTYLCWVP*EP---QTSKDKTIR

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	0.04 RPM	0.63 RPM
SRP017611_brain	0.00 RPM	1.67 RPM
SRP017611_kidney	0.00 RPM	8.32 RPM
SRP017611_liver	0.07 RPM	0.07 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1250 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1250 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1250 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003238	1 retrocopy	retro_cfam_1250 ,
Canis familiaris	ENSCAFG00000024818	1 retrocopy	retro_cfam_1824,
Mustela putorius furo	ENSMPUG00000007888	1 retrocopy	retro_mputfur_1331,