RetrogeneDB ID: retro_cfam_58

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 24:36440444..36441017(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000011481
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000005582
• Aliases: IFNL1, IL29
• Description: None

Sequence

>retro_cfam_58
ATGGCTACAGCTCGGGTCCTGGTGCTGGTGACCGTGGTGCTGGGCTTGACCAGAGCCGGCCCTGTCCCTACTTCCAAACC
CACCACAACCAGGAGGGGCTGCCACATGGACAGGTTCCAGTCTCTGTCACCCAGGGAGCTAGAAGCCTTCAAGAAGGCCA
AGGATGCCTTGGAAGAGTCGCTCTCCTGGAAGAACTGGAGCTGCAGCTCTCGCCTCTTCCCTAGATCCAGGGACCTGAGA
CTCCTGCAGGCCTGGGAGCGTCCTGTGGCCTTGGAGGCTGAGCTAGACTTGACACTGAAGGTCCTGGAGAACATGACTGA
CTCATCGCTGGGGGTGACCCTGGACCAGCCCCTCCGCACGCTGCACCACATCCACTCGGAGCTCCAGGCTTGTGTCCCGG
CTCAGCCCACAGCAGACCCCAGGCCCCACGGCCGCCTCCACCACTGGCTGCACCGGCTCCAGAAGGCCCCCAAGGAGTCC
CAGGGCTGCCTCGAGGCCTCCATCACGTTCAACCTCTTCCGCCTCCTCACACGGGACCTGAAATGTGTTGCCAGTAGAGA
CCTGTGCGTCTGA

Alignment

ORF - retro_cfam_58 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.44 %
• Parental protein coverage: 96.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAIAWVLVLVTAGLSLARAGPVPTSKPTTAWRGCDIGRFKSLSPRELEAFKKAKDALEYSL--KNWSCNS
          MA.A.VLVLVT..L.L.RAGPVPTSKPTT..RGC...RF.SLSPRELEAFKKAKDALE.SL..KNWSC.S
Retrocopy MATARVLVLVTVVLGLTRAGPVPTSKPTTTRRGCHMDRFQSLSPRELEAFKKAKDALEESLSWKNWSCSS

Parental  RLFPRNRDLRQLQVWERPVALEAELALTLKVLETMADRSLGDILDQPLHTLRHIHSQLQACVKAQPPAGP
          RLFPR.RDLR.LQ.WERPVALEAEL.LTLKVLE.M.D.SLG..LDQPL.TL.HIHS.LQACV.AQP.A.P
Retrocopy RLFPRSRDLRLLQAWERPVALEAELDLTLKVLENMTDSSLGVTLDQPLRTLHHIHSELQACVPAQPTADP

Parental  QPRGRLHPWLHRLHEASKKESQGCLEASVLFNLFRLLKKDLECVAVGDLCV
          .P.GRLH.WLHRL..A..KESQGCLEAS..FNLFRLL..DL.CVA..DLCV
Retrocopy RPHGRLHHWLHRLQKA-PKESQGCLEASITFNLFRLLTRDLKCVASRDLCV

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	0.04 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_58 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_58 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_58 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_56

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008614	1 retrocopy	retro_amel_68,
Canis familiaris	ENSCAFG00000005582	1 retrocopy	retro_cfam_58 ,
Equus caballus	ENSECAG00000005085	1 retrocopy	retro_ecab_56,
Felis catus	ENSFCAG00000010737	1 retrocopy	retro_fcat_111,
Monodelphis domestica	ENSMODG00000023790	1 retrocopy	retro_mdom_1793,
Mustela putorius furo	ENSMPUG00000017733	1 retrocopy	retro_mputfur_164,