RetrogeneDB ID: retro_cfam_1528

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 33:8104192..8104722(-)
• Located in intron of: ENSCAFG00000009622

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000000399
• Aliases: None
• Description: None

Sequence

>retro_cfam_1528
GAAAAGGTCAAACTCTTTGGTCCTCTGGGGATGAAAGTGAAGAACATAGAGTTCTTGGAGAGACAGATGGAAACTCTGAA
AGACCTGCTGGAAGAGCTCAAAAACAAACTTCTTGACATCAAAGCAGAGACTTTCACTAACAGCAATTCTCTCACCAAGG
AGGATAGGATGATGTGTGAGTTTGGGGCCATCAGACACACCAGTGGATCCTGGCAGTTTGGCTTCAATGGGTGGATAACC
TACCTCTTTGATTCAGAGAACAGAAAGTGGACAGTGGTTCATCCTGGAGACAGATCATGAAAGGCTACTGTTGGACAGTG
ACAGAGATGTGACCAACTTCCTCATGAAGATCTCAAAGAGAAGTTCTAAAAGCTGGCTCAAGCCAAGTACTGGTGCACTG
GGATGAAACGCCAGGGACAGTAGTACCACTAACCGCGCCTCAAGGCATGGCCCAGTCCAGGGCCTCAGCCATCAGACCTG
GCACCCGGGTCTTCCCCCTCTTCCTCAGCTGTGCAATCATAATTGGCATC

Alignment

ORF - retro_cfam_1528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.12 %
• Parental protein coverage: 80.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KELTLVGPMRTRMNDTGFRETQKETLNDLMEELQKKVRDIKAEIYPKNGSLDLHGEMKCVRGASRYTSAS
          ....L.GP.........F.E.Q.ETL.DL.EEL..K..DIKAE......SL.....M.C..GA.R.TS.S
Retrocopy EKVKLFGPLGMKVKNIEFLERQMETLKDLLEELKNKLLDIKAETFTNSNSLTKEDRMMCEFGAIRHTSGS

Parental  WKFAFNGQITHLFDSENGKWTVLQPAGRQFQGT-LDSDRDVTNFLTKVSNGDCKSWME-YIMNHWDEKLE
          W.F.FNG.IT.LFDSEN.KWTV..P..R....T.LDSDRDVTNFL.K.S....KSW.......HWDE...
Retrocopy WQFGFNGWITYLFDSENRKWTVVHPGDRS*KAT>LDSDRDVTNFLMKISKRSSKSWLK>QVLVHWDETPG

Parental  TTVPQSRPQDMAPSGASGSAPSTWIFLLFLYCAILLGI
          T.VP...PQ.MA.S.AS...P.T..F.LFL.CAI..GI
Retrocopy TVVPLTAPQGMAQSRASAIRPGTRVFPLFLSCAIIIGI

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	0.25 RPM
SRP017611_brain	0.40 RPM	1.35 RPM
SRP017611_kidney	0.00 RPM	0.99 RPM
SRP017611_liver	0.00 RPM	0.73 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1528 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1528 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1528 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	ENSCAFG00000000399	2 retrocopies	retro_cfam_1528 , retro_cfam_432,
Myotis lucifugus	ENSMLUG00000025468	1 retrocopy	retro_mluc_1324,
Ictidomys tridecemlineatus	ENSSTOG00000001385	1 retrocopy	retro_itri_597,