RetrogeneDB ID: retro_cfam_754

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 17:29375615..29376326(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DERL1
• Ensembl ID: ENSCAFG00000000974
• Aliases: None
• Description: derlin 1 [Source:HGNC Symbol;Acc:28454]

Sequence

>retro_cfam_754
CTAACATGCTGTTGGTTGGTCACTACTGTTGCAGTGCCCTCGTTGGCAAACCTGGTCTCATCAGCCTACTACTTCTTCTT
CTGGCCTGAAGAAGCCTTCCTCTATTGCTTCCAGATTTGGAGGCCAATCACTGCTACTTTTTATTTCCCCATGGATCCAG
GAATTGGATTTCTTTATTTGGTCAATTTATATTTCTTATATCAATATTCTACATGCCTTAAAACAGGAGCTTTTGATGGG
AGGCCAGCTGGCTATTTATTCATGCTCCTCTTTAACTGGATTTGCATCGTGATTACGGGCTTAGCAACGAATATGCATTT
GTTGATGATTCCTCCTATCATGTCAGTACTTTATGTCTGGGCACAGCTGAACAGAGACATGATCATATCACTTTCATTTG
GAACACAAATGAAGACCTGTTATTTACCATCGGTTATTCTTGGATTCAACTATATCATGGGAGGCTCGGTAAGCAATGAG
CTCGTTGGAAATCTTGTTGGACATCTTTATTTCCTCCTAATGTTCAGATACCCAGTGGACTTGCAATGAAAAAATTTGGT
ATCCATACCTCAGTTTTTGTACCCACTGCCTAGCCAGCAGGAGAGGGGAGGAGTGTCAGGGTTTGGTGTGCCCCCCATTA
GCATGGGGAGAGTTGCTGATCAGAAGAGTCAAGGCAGGAGACACAACTGGAGACAGGACTTCTGACTTGGT

Alignment

ORF - retro_cfam_754 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.06 %
• Parental protein coverage: 94.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITRYWFAATVAVPLVGKLGLISPAYFFLWPE-AFLYRFQVWRPITATFYFPVGPGTGFLYLVNLYFLYQY
          .T..W...TVAVP....L...S..YFF.WPE.AFLY.FQ.WRPITATFYFP..PG.GFLYLVNLYFLYQY
Retrocopy LTCCWLVTTVAVPSLANL-VSSAYYFFFWPEEAFLYCFQIWRPITATFYFPMDPGIGFLYLVNLYFLYQY

Parental  STRLETGAFDGRPADYLFMLLFNWICIVITGLAMDMQLLMIPLIMSVLYVWAQLNRDMIVSFWFGTRFKA
          ST.L.TGAFDGRPA.YLFMLLFNWICIVITGLA..M.LLMIP.IMSVLYVWAQLNRDMI.S..FGT..K.
Retrocopy STCLKTGAFDGRPAGYLFMLLFNWICIVITGLATNMHLLMIPPIMSVLYVWAQLNRDMIISLSFGTQMKT

Parental  CYLPWVILGFNYIIGGSVINELIGNLVGHLYFFLMFRYPMDLGGRNFLSTPQFLYRWLPSR--RGGVSGF
          CYLP.VILGFNYI.GGSV.NEL.GNLVGHLYF.LMFRYP.DL...N..S.PQFLY..LPS...RGGVSGF
Retrocopy CYLPSVILGFNYIMGGSVSNELVGNLVGHLYFLLMFRYPVDLQ*KNLVSIPQFLYP-LPSQQERGGVSGF

Parental  GVPPASMRRAADQNGGGGRHNWGQGFRLG
          GVPP.SM.R.ADQ...G.RHNW.Q.F.LG
Retrocopy GVPPISMGRVADQKSQGRRHNWRQDF*LG

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	67.03 RPM
SRP017611_brain	0.00 RPM	39.30 RPM
SRP017611_kidney	0.00 RPM	54.41 RPM
SRP017611_liver	0.00 RPM	36.33 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_754 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_754 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_754 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006519	1 retrocopy	retro_amel_364,
Canis familiaris	ENSCAFG00000000974	1 retrocopy	retro_cfam_754 ,
Cavia porcellus	ENSCPOG00000011870	1 retrocopy	retro_cpor_1520,
Myotis lucifugus	ENSMLUG00000009085	1 retrocopy	retro_mluc_2035,
Mustela putorius furo	ENSMPUG00000001132	1 retrocopy	retro_mputfur_1082,
Mus musculus	ENSMUSG00000022365	1 retrocopy	retro_mmus_919,
Rattus norvegicus	ENSRNOG00000005551	2 retrocopies	retro_rnor_1206, retro_rnor_2717,
Sarcophilus harrisii	ENSSHAG00000011915	1 retrocopy	retro_shar_588,