RetrogeneDB ID: retro_rnor_2717

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:7795720..7796338(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Derl1
• Ensembl ID: ENSRNOG00000005551
• Aliases: Derl1, RGD1311835
• Description: derlin-1 [Source:RefSeq peptide;Acc:NP_001014224]

Sequence

>retro_rnor_2717
TTCCTCTATCGCTTCCAGATATGGAGGCCGTTCACTGCCGCCTTTTATTTCCCCGTGGGGCCTGGAACTGGATTTCTTTA
TTTGGTCAATTTAAATTTCTTATATAAGTATTCTACACGGCTTGAGGCAGGAGCTTTTGACAGGAGGCCAGCAGACTATT
TATTCATGCTTCTCTTCAACTGGATTTGCATTACTATTACTGGCTTAGCCATGGATATGCAGTTGCTGATGATTCCTCAA
ATCATGTCAGTACTTTACATCTGGGCCCAACTGAACAGAGACCTGATTCTATCATTTTGGTTTGGAACACGATTTAAGGC
CTGTTACTTACCTTGGGTTATCCTCGGATTCAACTATATCATTGGAGGCTCGGTCATCAATGAGCTCATTGGAAACCTTG
TCGGACATCTTCATTTCTTCCTGATGTTCAGATACCCAATGGATTTGAGAGGAAGGAATTTCCTGTCCACACCTCAGTTT
TTGTACCACTGGCTACCCAGCAGGAGAGGAGGGGTGTCGGGGTTTGGTGTGCGCCCTGCAAGCATGAGGCGAGCTGCTGA
TCAGAATGGCGGAGGCAGGAGACACAACTGGGGCCAGGGCTTCCGACTTGGAGAGCGG

Alignment

ORF - retro_rnor_2717 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.72 %
• Parental protein coverage: 82.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLYRFQIWRPFTATFYFPVGPGTGFLYLVNLYFLYQYSTRLEAGAFDGRPADYLFMLLFNWICIVITGLA
          FLYRFQIWRPFTA.FYFPVGPGTGFLYLVNL.FLY.YSTRLEAGAFD.RPADYLFMLLFNWICI.ITGLA
Retrocopy FLYRFQIWRPFTAAFYFPVGPGTGFLYLVNLNFLYKYSTRLEAGAFDRRPADYLFMLLFNWICITITGLA

Parental  MDMQLLMIPLIMSVLYVWAQLNRDLIVSFWFGTRFKACYLPWVILGFNYIIGGSVINELIGNLVGHLYFF
          MDMQLLMIP.IMSVLY.WAQLNRDLI.SFWFGTRFKACYLPWVILGFNYIIGGSVINELIGNLVGHL.FF
Retrocopy MDMQLLMIPQIMSVLYIWAQLNRDLILSFWFGTRFKACYLPWVILGFNYIIGGSVINELIGNLVGHLHFF

Parental  LMFRYPMDLGGRNFLSTPQFLYRWLPSRRGGVSGFGVPPASMRRAADQNGGGGRHNWGQGFRLGDQ
          LMFRYPMDL.GRNFLSTPQFLY.WLPSRRGGVSGFGV.PASMRRAADQNGGG.RHNWGQGFRLG..
Retrocopy LMFRYPMDLRGRNFLSTPQFLYHWLPSRRGGVSGFGVRPASMRRAADQNGGGRRHNWGQGFRLGER

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
SRP017611_brain	0.00 RPM	50.04 RPM
SRP017611_kidney	0.00 RPM	87.65 RPM
SRP017611_liver	0.00 RPM	75.44 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2717 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2717 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2717 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,