RetrogeneDB ID: retro_cfam_863

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 19:13609131..13609467(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED31
• Ensembl ID: ENSCAFG00000023445
• Aliases: None
• Description: mediator complex subunit 31 [Source:HGNC Symbol;Acc:24260]

Sequence

>retro_cfam_863
CAGTTGGAGCTGGAATTTTGCAGTGCTAGCTAACCCCAATTACCTTAACTTTCTTGTCCAAAGAAAGGTTACTTCAAAGA
AAAAGCCTTTGTTAATTATCTTAAGTATTTGTTCTACTGAAAAGATCCAGAATATGCCAAGTATCTAAAGTACCCTCAGT
GTTTGCATATGTTAGAACTGCTTCAGTATGAACACTTCCACAAGGAGCTGGTGAATGCTCAGTGCACCAGGTTTATTGAC
AAGCAGCAGATTCTGCATTGGCAGCACTACTCACAGAAGCAGATGCTCCTTCAGCAAGCCCTGGCCAAGCAGCAGCAGAA
TCAAGCGGTGGGAAAA

Alignment

ORF - retro_cfam_863 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.52 %
• Parental protein coverage: 86.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QLELEF-VQC-LANPNYLN-FLAQ-RGYFKDKAFVNYLKYLLYWKEPEYAKYLNY-QCLHGKDPIPHYDT
          QLELEF..QC.LANPNYLN.FL....GYFK.KAFVNYLKYL.Y.K.PEYAKYL.Y.QCLH..........
Retrocopy QLELEF<LQC<LANPNYLN>FLSK>KGYFKEKAFVNYLKYLFY*KDPEYAKYLKYPQCLHMLELLQYEHF

Parental  SQGAVNAQCAKFIDEQQILHWQHYSRKRMRLQQALAEQQQQNHAAGK
          ....VNAQC..FID.QQILHWQHYS.K.M.LQQALA..QQQN.A.GK
Retrocopy HKELVNAQCTRFIDKQQILHWQHYSQKQMLLQQALA-KQQQNQAVGK

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	12.26 RPM
SRP017611_brain	0.16 RPM	9.13 RPM
SRP017611_kidney	1.39 RPM	56.33 RPM
SRP017611_liver	0.00 RPM	2.68 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_863 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_863 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_863 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000023445	1 retrocopy	retro_cfam_863 ,
Myotis lucifugus	ENSMLUG00000010814	1 retrocopy	retro_mluc_1682,
Mus musculus	ENSMUSG00000020801	2 retrocopies	retro_mmus_1479, retro_mmus_3201,