RetrogeneDB ID: retro_rnor_124

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:73290612..73291833(+)
• Located in intron of: ENSRNOG00000003063

Retrocopy information

• Ensembl ID: ENSRNOG00000003062
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: KLHDC2
• Ensembl ID: ENSRNOG00000004474
• Aliases: None
• Description: Kelch domain-containing protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q3KRE6]

Sequence

>retro_rnor_124
ATGGCTGATGGCAACGAGGATGCTCGAGCGGAGGACATGCCAGGCCCGGCCTTCGAAGGCTATGAGGCCATGGAGCTGGC
CTGCCCGGCCGAGCGCAGCGGCCACGTCGCTGTCAGCGATGGGCGCCACATGTTCGTCTGGGGCGGCTACAAGAGTAATC
AAGTGAGAGGACTCTATGACTTCTATCTGCCCAGAGAAGAACTGTGGATCTACAACATGGAGAGTGGAAGATGGAAAAAG
ATCAACACTGAAGGTGATGTGCCCCCGTCCATGTCTGGGAGCTGCGCTGTGTGCGTAGACAGGGTGCTGTACTTGTTTGG
AGGCCACCATTCCAGAGGCAACACAAACAAGTTCTACATGCTGGACTCAAGGTCTGCAGACAGAGTGTTACAGTGGGAAA
GAATTGATTGCCAAGGAATTCCTCCATCATCAAAGGACAAACTTGGTGTCTGGGTATATAAAAACAAGTTAATATTTTTT
GGAGGCTATGGATATATACCTGAAGATAAAGTATTGGGGACGTTTGAATTTGATGAAACATCTTTTCGGAATTCAAGTCA
TCCAAGAGGATGGAATGATCATGTCCATATTTTAGACACTGAAACATTTGCCTGGAGCCAGCCCATCACCACTGGCAAGG
CACCTTCACCTCGTGCTGCCCATGCCTGTGCAACTGTTGGAAACAAGGGTTTTGTGTTTGGTGGCAGATACCGAGATACT
AGAATGAATGATCTGCACTATCTTAATCTGGACACATGGGAGTGGAATGAACTAATTCCACAAGGTATATGCCCTGTTGG
CCGCTCCTGGCACTCACTGACAGCAGTCTCTTCAGACCATCTTTTTCTCTTCGGAGGATTTACCACTGAAAAGCAGCCAC
TAAGTGATGCCTGGACTTACTGCATCAGTAAAAATGAATGGATTCAGTTTAATCATTCTTATGTTGAAAAACCAAGATTA
TGGCATACAGCTTGTGCGAGCGATGAGGGAGAAGTAATTGTTTTTGGTGGTTGTGCCAACAATCTGCTGGTCCATCATAG
GGCTGCACACAGTAACGAAGTACTTATATTTTCAGTCCAACCAAAATCTCTTGTACGGCTAAGCTTAGAAGCAGTCATTT
GCTTTAAAGATATGCTAGCCAACTCGTGGAGCTGCCTTCCAAAACACTTACTTCACAGTGTTAATCAGAGGTTTGGTAGT
AACAACAGTTCTGGATCATAA

Alignment

ORF - retro_rnor_124 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADGNEDARAEDMPGPAFEGYEAMELACPAERSGHVAVSDGRHMFVWGGYKSNQVRGLYDFYLPREELWI
          MADGNEDARAEDMPGPAFEGYEAMELACPAERSGHVAVSDGRHMFVWGGYKSNQVRGLYDFYLPREELWI
Retrocopy MADGNEDARAEDMPGPAFEGYEAMELACPAERSGHVAVSDGRHMFVWGGYKSNQVRGLYDFYLPREELWI

Parental  YNMETGRWKKINTEGDVPPSMSGSCAVCVDRVLYLFGGHHSRGNTNKFYMLDSRSADRVLQWERIDCQGI
          YNME.GRWKKINTEGDVPPSMSGSCAVCVDRVLYLFGGHHSRGNTNKFYMLDSRSADRVLQWERIDCQGI
Retrocopy YNMESGRWKKINTEGDVPPSMSGSCAVCVDRVLYLFGGHHSRGNTNKFYMLDSRSADRVLQWERIDCQGI

Parental  PPSSKDKLGVWVYKNKLIFFGGYGYLPEDKVLGTFEFDETSFWNSSHPRGWNDHVHILDTETFAWSQPIT
          PPSSKDKLGVWVYKNKLIFFGGYGY.PEDKVLGTFEFDETSF.NSSHPRGWNDHVHILDTETFAWSQPIT
Retrocopy PPSSKDKLGVWVYKNKLIFFGGYGYIPEDKVLGTFEFDETSFRNSSHPRGWNDHVHILDTETFAWSQPIT

Parental  TGKAPSPRAAHACATVGNKGFVFGGRYRDARMNDLHYLNLDTWEWNELIPQGICPVGRSWHSLTPVSSDH
          TGKAPSPRAAHACATVGNKGFVFGGRYRD.RMNDLHYLNLDTWEWNELIPQGICPVGRSWHSLT.VSSDH
Retrocopy TGKAPSPRAAHACATVGNKGFVFGGRYRDTRMNDLHYLNLDTWEWNELIPQGICPVGRSWHSLTAVSSDH

Parental  LFLFGGFTTEKQPLSDAWTYCISKNEWIQFNHPYVEKPRLWHTACASDEGEVIVFGGCANNLLVHHRAAH
          LFLFGGFTTEKQPLSDAWTYCISKNEWIQFNH.YVEKPRLWHTACASDEGEVIVFGGCANNLLVHHRAAH
Retrocopy LFLFGGFTTEKQPLSDAWTYCISKNEWIQFNHSYVEKPRLWHTACASDEGEVIVFGGCANNLLVHHRAAH

Parental  SNEVLIFSVQPKSLVRLSLEAVICFKEMLANSWSCLPKHLLHSVNQRFGSNNTSGS
          SNEVLIFSVQPKSLVRLSLEAVICFK.MLANSWSCLPKHLLHSVNQRFGSNN.SGS
Retrocopy SNEVLIFSVQPKSLVRLSLEAVICFKDMLANSWSCLPKHLLHSVNQRFGSNNSSGS

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	0.43 RPM	59.39 RPM
SRP017611_kidney	0.07 RPM	26.94 RPM
SRP017611_liver	0.00 RPM	16.41 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_124 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_124 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000007045	1 retrocopy	retro_mmur_331,
Rattus norvegicus	ENSRNOG00000004474	1 retrocopy	retro_rnor_124 ,