RetrogeneDB ID: retro_cfam_1488

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:3069560..3069955(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000023995
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNF8
• Ensembl ID: ENSCAFG00000016893
• Aliases: None
• Description: SNF8, ESCRT-II complex subunit [Source:HGNC Symbol;Acc:17028]

Sequence

>retro_cfam_1488
ATGCATTGCTGTGGGGTGGGAACCGGCGTCACTGCCAAGAAGCTTGCTGAGGCCAAGTATAAGGAGCAAGGAACTGTCTT
GGCTGAGGACCAGCTAGCCCACATGTCGAAGCAGCTGGACATGCTCAAGACCAGTCTGGAGGAATTTACCAGCAAGCACA
AGCAGGCAATCCGGAAGAAGCTTGAGTTCTGGGTGCAGTTCCAGGGAATATCTTGTGTGACATGTGTGCCACCGCTGGCA
TGGATCCTCTGCCTTCTGGAAAAGGATTTTGGTCTGAGATGATAGGTGTGGGAGCTGAGAGTCCCGATTATTGAAGTGTG
TGAGGCTCTGAAGCATAGGATGGAGGTCCGATACCTCTGGGTGAACTACAGCAGCATGTGTTTAAGGGAAGGGGC

Alignment

ORF - retro_cfam_1488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.97 %
• Parental protein coverage: 51.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MHRRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQD
          MH..GVG.G..A.KKLAEAKYKE.GTVLAEDQLA.MSKQLDM.KT.LEEF.SKHKQ.IRK..EF.VQFQ.
Retrocopy MHCCGVGTGVTA-KKLAEAKYKEQGTVLAEDQLAHMSKQLDMLKTSLEEFTSKHKQAIRKKLEFWVQFQG

Parental  MCATIGVDPLA-SGKGFWSEML-GVGDFYYELGVQIIEVCLALKHR-NGGLITLEELHQQVLKGRG
          ......V.PLA.....FW...L.G......EL.V.IIEVC.ALKHR..GG.I.L.EL.Q.V.KGRG
Retrocopy ISCVTCVPPLA>GSSAFWKRIL<GLR**VWELRVPIIEVCEALKHR<DGGPIPLGELQQHVFKGRG

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	26.04 RPM
SRP017611_brain	0.00 RPM	16.99 RPM
SRP017611_kidney	0.00 RPM	35.20 RPM
SRP017611_liver	0.00 RPM	14.94 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1488 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1488 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005062	1 retrocopy	retro_amel_164,
Canis familiaris	ENSCAFG00000016893	1 retrocopy	retro_cfam_1488 ,
Choloepus hoffmanni	ENSCHOG00000013760	1 retrocopy	retro_chof_1372,
Callithrix jacchus	ENSCJAG00000007322	2 retrocopies	retro_cjac_1175, retro_cjac_1922,
Echinops telfairi	ENSETEG00000000758	1 retrocopy	retro_etel_709,
Felis catus	ENSFCAG00000008944	2 retrocopies	retro_fcat_1291, retro_fcat_574,
Homo sapiens	ENSG00000159210	1 retrocopy	retro_hsap_2394,
Gorilla gorilla	ENSGGOG00000025290	1 retrocopy	retro_ggor_1816,
Macropus eugenii	ENSMEUG00000016638	1 retrocopy	retro_meug_663,
Mustela putorius furo	ENSMPUG00000015356	1 retrocopy	retro_mputfur_1425,
Mus musculus	ENSMUSG00000006058	1 retrocopy	retro_mmus_1050,
Nomascus leucogenys	ENSNLEG00000002743	1 retrocopy	retro_nleu_2520,
Oryctolagus cuniculus	ENSOCUG00000009156	2 retrocopies	retro_ocun_814, retro_ocun_996,
Pongo abelii	ENSPPYG00000008911	1 retrocopy	retro_pabe_2161,
Tarsius syrichta	ENSTSYG00000004576	1 retrocopy	retro_tsyr_843,