RetrogeneDB ID: retro_cfam_877

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:42132495..42132933(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THYN1
• Ensembl ID: ENSCAFG00000009772
• Aliases: None
• Description: thymocyte nuclear protein 1 [Source:HGNC Symbol;Acc:29560]

Sequence

>retro_cfam_877
GCCTCTAAAAAATGTGGGAAGAATCTAAAGAGTTACTGGTTGAAAAAAGTCAGAGCTAGAAAGCGACTAGAGAAAGGTGT
ACATGGGAAGTTTGCACTGAGTATCCTAAAGCCAGCCCAATCAGACAGCATGCTGGGATGGTGTTCCCAACTGGCAGGAC
AGGCTGGCAACTTCCTTCCAACCATGAAGCTAAAGGAAGAAGCCTTCTTCTACCATCACAACTGCAAAGAGCCAGGCATC
ACAGGACTTGTGAAGCTTGTCAAGGAGGCTTACTCAGACATCCCATAGTTTGAGAAAAACAATCCCCATTATGACCCATC
CGGCAAAGAAGACAACCTCAAATGGTCCGTGTTGGATGTACAATTTGTTCCCATGATGAAGTGTTTCATTACTCTAGCTG
AGCTTAAAACCCATCACTGAGCCCTTAAAAAATATGGC

Alignment

ORF - retro_cfam_877 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.9 %
• Parental protein coverage: 64.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASKNCGNNQSSYWLMKSEPQSRIEKGVDVKFSIEDLK-AEPKQTACWDGVRNYQARNFLRAMKLEQKAFF
          ASK.CG.N..SYWL.K.....R.EKGV..KF....LK.A.......W......QA.NFL..MKL...AFF
Retrocopy ASKKCGKNLKSYWLKKVRARKRLEKGVHGKFALSILKPAQSDSMLGWCSQLAGQAGNFLPTMKLKEEAFF

Parental  YHSNCKEPGIAGLVKIVKEAYPDHTQFEKNNPYYDPSSKEDNPKWSMVDVQFVRLMKRYITLTELKANHQ
          YH.NCKEPGI.GLVK.VKEAY.D...FEKNNP.YDPS.KEDN.KWS..DVQFV..MK..ITL.ELK..H.
Retrocopy YHHNCKEPGITGLVKLVKEAYSDIP*FEKNNPHYDPSGKEDNLKWSVLDVQFVPMMKCFITLAELKTHH*

Parental  AHKATG
          A.K..G
Retrocopy ALKKYG

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	6.59 RPM
SRP017611_brain	0.00 RPM	4.84 RPM
SRP017611_kidney	0.00 RPM	3.57 RPM
SRP017611_liver	0.00 RPM	1.74 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_877 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_877 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_877 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007294	1 retrocopy	retro_amel_300,
Canis familiaris	ENSCAFG00000009772	1 retrocopy	retro_cfam_877 ,
Cavia porcellus	ENSCPOG00000006567	1 retrocopy	retro_cpor_1542,
Felis catus	ENSFCAG00000007419	1 retrocopy	retro_fcat_946,
Macropus eugenii	ENSMEUG00000008297	1 retrocopy	retro_meug_287,
Mustela putorius furo	ENSMPUG00000009185	1 retrocopy	retro_mputfur_1114,