RetrogeneDB ID: retro_cfam_1789

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 6:23694299..23694528(+)
• Located in intron of: ENSCAFG00000017787

Retrocopy information

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

Parental gene information

• Parental gene symbol: NEDD8
• Ensembl ID: ENSCAFG00000012097
• Aliases: None
• Description: neural precursor cell expressed, developmentally down-regulated 8 [Source:HGNC Symbol;Acc:7732]

Sequence

>retro_cfam_1789
AAGACACTGATCGGAAAGGAGAATGAGGTTGACATTGAACCCACAGACAAGGTGGAGCGAATCAAGGAGCGTGTGGAGGA
GAAAGAGGGAATCCCCCACAGCAGCACAGCGGCTCATCTACAGTGGAAAACAGATGAATGATGAGAAGACAGCAGCTGAT
TACAAGATCTTAGATGGTTCAGTCCTCCACCTGGTGTCGGCTCTGAGAGGAGGAGGTGGTCTTAGGCAG

Alignment

ORF - retro_cfam_1789 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.01 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQ-QRLIYSGKQMNDEKTAADYKILGGSVLHLVLALR
          .TL.GKE.E.DIEPTDKVERIKERVEEKEGIP....QRLIYSGKQMNDEKTAADYKIL.GSVLHLV.ALR
Retrocopy KTLIGKENEVDIEPTDKVERIKERVEEKEGIPHSS>QRLIYSGKQMNDEKTAADYKILDGSVLHLVSALR

Parental  GGGGLRQ
          GGGGLRQ
Retrocopy GGGGLRQ

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	60.77 RPM
SRP017611_brain	0.24 RPM	33.27 RPM
SRP017611_kidney	0.46 RPM	77.40 RPM
SRP017611_liver	0.00 RPM	12.76 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1789 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1789 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1789 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000038842	1 retrocopy	retro_btau_89,
Canis familiaris	ENSCAFG00000012097	1 retrocopy	retro_cfam_1789 ,
Choloepus hoffmanni	ENSCHOG00000001228	5 retrocopies	retro_chof_1012, retro_chof_1616, retro_chof_2696, retro_chof_613, retro_chof_788,
Callithrix jacchus	ENSCJAG00000006876	1 retrocopy	retro_cjac_4064,
Cavia porcellus	ENSCPOG00000010930	1 retrocopy	retro_cpor_371,
Gorilla gorilla	ENSGGOG00000016105	1 retrocopy	retro_ggor_261,
Monodelphis domestica	ENSMODG00000003254	1 retrocopy	retro_mdom_1681,