RetrogeneDB ID: retro_cfam_458

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:32228480..32228840(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000001473
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MED8
• Ensembl ID: ENSCAFG00000005237
• Aliases: None
• Description: mediator complex subunit 8 [Source:HGNC Symbol;Acc:19971]

Sequence

>retro_cfam_458
ATCACCCTGCAGAGGGAGGAGAAGCAGCTGGAGGCATCATTAGATGCACTGCTGAGTCAAGTGGCTGATCTGAAGAACTC
ACTGGAGAGTTTCATATACAAGTTGGAGAACGAGTATGACCGGCTGACCTGGCCGTCTGTCCTGGACAGCTTCGCCTTGC
TCTCCGGACAGTTGAACACTTTGAACAAGGTCTTGAAGCATGAAAAGACACCGCTGTTCCGCAACCAGGCCATCATCCCC
CTGCTGCTGTCCTCAGACCGTGATGAAGATCTCATGCGGCAGACCCAAGGACGAGTGCCTGTTTTCAGCCACGAGGTGGT
CCCTGACCACCTGAGAACCAAGCCTGACCCTGAGGTCGAA

Alignment

ORF - retro_cfam_458 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.33 %
• Parental protein coverage: 51.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLVQREEKQLEASLDALLSQVADLKNSLGSFIYKLENEYDRLTWPSVLDSFALLSGQLNTLNKVLKHEKT
          ...QREEKQLEASLDALLSQVADLKNSL.SFIYKLENEYDRLTWPSVLDSFALLSGQLNTLNKVLKHEKT
Retrocopy ITLQREEKQLEASLDALLSQVADLKNSLESFIYKLENEYDRLTWPSVLDSFALLSGQLNTLNKVLKHEKT

Parental  PLFRNQVIIPLVLSPDRDEDLMRQTEGRVPVFSHEVVPDHLRTSGLQQVQ
          PLFRNQ.IIPL.LS.DRDEDLMRQT.GRVPVFSHEVVPDHLRT.....V.
Retrocopy PLFRNQAIIPLLLSSDRDEDLMRQTQGRVPVFSHEVVPDHLRTKPDPEVE

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	15.29 RPM
SRP017611_brain	0.08 RPM	15.48 RPM
SRP017611_kidney	0.20 RPM	15.78 RPM
SRP017611_liver	0.00 RPM	11.09 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_458 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_458 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_458 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005237	1 retrocopy	retro_cfam_458 ,
Macropus eugenii	ENSMEUG00000013567	1 retrocopy	retro_meug_1813,
Myotis lucifugus	ENSMLUG00000012621	1 retrocopy	retro_mluc_1618,
Monodelphis domestica	ENSMODG00000011310	1 retrocopy	retro_mdom_1131,
Oryctolagus cuniculus	ENSOCUG00000027895	2 retrocopies	retro_ocun_1088, retro_ocun_67,
Otolemur garnettii	ENSOGAG00000001865	1 retrocopy	retro_ogar_2091,
Ictidomys tridecemlineatus	ENSSTOG00000009737	1 retrocopy	retro_itri_818,