RetrogeneDB ID: retro_cfam_448

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:20745038..20745491(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCAFG00000028564
• Aliases: None
• Description: None

Sequence

>retro_cfam_448
CAGGCTCAGGTTCAAGGATCCCTCTCAGAGGCCTGTGGGGTTGCTATTAATTATATGGCATCTTACGAGCTGAACGTCAG
TGATGGTTATTTATCTATGGTCTGTTACTTCGATGAAGACCCGGATGCATCTGTTTATGTCCCCTTTTTCCAAAACCAAG
CTGAGGTGAAGAAAGAACACACAAGGCAGTTCATAAGATACCTGAAGGAGCATAAGAGTAAAGTCTGCCTTCCAGTGGTT
AAGAGGCTTGACAAAGAGTACTGAGGAACGAATGTACAAGCTATAGTGATGGCTTTGGAGTTGGAAAACGGGTTACACAA
GCTCCTGCAAGACCTGCAGAACTTGGCTTCTCAGAAGAATGAAACCGATCTCTTAGAATTCCTGAAAAGGTTCATGGGTA
AACAGAAGAGGAACATAAAATATCTGGAATACTAGCATAGCTATCAGAAGGAA

Alignment

ORF - retro_cfam_448 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.05 %
• Parental protein coverage: 87.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAQAQGPLSEACGVAINYIASYELNVSDGYLSMVCYFDEDPDAPVYVPFFQDQVEVKKGHARQFIRYLKE
          QAQ.QG.LSEACGVAINY.ASYELNVSDGYLSMVCYFDEDPDA.VYVPFFQ.Q.EVKK.H.RQFIRYLKE
Retrocopy QAQVQGSLSEACGVAINYMASYELNVSDGYLSMVCYFDEDPDASVYVPFFQNQAEVKKEHTRQFIRYLKE

Parental  RKSKVCLPVVKRLDKEYWGTNVQAIVMALELENGLHKLLQDLQNLASQKNETDLLEFLKRFVGKQKRNIK
          .KSKVCLPVVKRLDKEY.GTNVQAIVMALELENGLHKLLQDLQNLASQKNETDLLEFLKRF.GKQKRNIK
Retrocopy HKSKVCLPVVKRLDKEY*GTNVQAIVMALELENGLHKLLQDLQNLASQKNETDLLEFLKRFMGKQKRNIK

Parental  YLEYQHSYQKE
          YLEY.HSYQKE
Retrocopy YLEY*HSYQKE

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	0.00 RPM
SRP017611_brain	0.08 RPM	0.00 RPM
SRP017611_kidney	0.26 RPM	0.07 RPM
SRP017611_liver	0.58 RPM	0.00 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_448 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_448 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_448 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015497	1 retrocopy	retro_amel_333,
Canis familiaris	ENSCAFG00000028564	9 retrocopies	retro_cfam_1158, retro_cfam_1163, retro_cfam_1432, retro_cfam_1901, retro_cfam_365, retro_cfam_448 , retro_cfam_567, retro_cfam_715, retro_cfam_746,
Ictidomys tridecemlineatus	ENSSTOG00000022867	1 retrocopy	retro_itri_1495,