RetrogeneDB ID: retro_rnor_1206

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:88401629..88402095(+)
• 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_1206
GCCAGCAGAATATTCATGCTTCTCTTTAACTGGATCTGCTTTGTTATTATTGGCTTAGCCATGGATATGCAGTTGTTGAT
GATTCCTCTGATCATGTCAGTACTTTATGTCTGGGCCCAGCTGAACAGAGACCTGATTGTATCATTTGGTTTGGAACATG
ATTTTAGGCCTGTTTACTTACCTTGGGTTATCCTTGGATTCAACTGTATCGTTAGAGGCTCTTGATCAATGAGCTCATTG
GAAATCTTGTCAGACATCTTTATTTCTTCCTGATGTTCAGATACCCTATGGACTTGGGAGGAAGGAATTTTCTGTCCACA
CTTCAGTGTTTGTACCGCTGGCAAGGGCGTAGGAGAGCAAGGGTGTCAGGGTTTGGTGTGCCGGCTGTGAGCATGAGGCA
AGCTGCTGATCAGAATGGGGGAGGCGGGAGACAAACTGGGGCCATGGCTTCCTTATTAGAGACCAG

Alignment

ORF - retro_rnor_1206 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.62 %
• Parental protein coverage: 62.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ADYLFMLLFNWICIVITGLAMDMQLLMIPLIMSVLYVWAQLNRDLIVSF-WFGTRFKAC-YLPWVILGFN
          A...FMLLFNWIC.VI.GLAMDMQLLMIPLIMSVLYVWAQLNRDLIVSF.WFGT.F.AC.YLPWVILGFN
Retrocopy ASRIFMLLFNWICFVIIGLAMDMQLLMIPLIMSVLYVWAQLNRDLIVSF<WFGT*F*AC>YLPWVILGFN

Parental  YIIGGS-VINELIGNLVGHLYFFLMFRYPMDLGGRNFLSTPQFLYRWLPSRRGGVSGFGVPPASMRRAAD
          .I..GS..INELIGNLV.HLYFFLMFRYPMDLGGRNFLST.Q.LYRW...RR..VSGFGVP..SMR.AAD
Retrocopy CIVRGS<LINELIGNLVRHLYFFLMFRYPMDLGGRNFLSTLQCLYRWQGRRRARVSGFGVPAVSMRQAAD

Parental  QNGGGGRH-NWGQGFRLGDQ
          QNGGGGR..NWG.GF...DQ
Retrocopy QNGGGGRQ<NWGHGFLIRDQ

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_1206 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1206 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1206 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,