RetrogeneDB ID: retro_rnor_1060

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:70387925..70388440(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kdelr1
• Ensembl ID: ENSRNOG00000021082
• Aliases: None
• Description: ER lumen protein retaining receptor 1 [Source:UniProtKB/Swiss-Prot;Acc:Q569A6]

Sequence

>retro_rnor_1060
AGCCAAGTCCTGTTACTATGGTGTTCACTACCTGATATCTGGACCTGTTCACCAACTACATTTCACTCTACAATACCTGC
ATAAATGTGGTCTACATAGCTTGTTCCTTTACCATAGTGTGGATGATCTACAGCAAGTTCAAAGCTACTTATGGTGGAAA
CCATGAACTTTCCAGGTGGAGTTCTTCGTTGTTCCTACTGCTATTTTGACATTCAAAAATAGCATTACTTCACCCCTCTG
GAGATTCTATGGACTTTCTCCATGGAGTCAGTGACTATCTTGCCACGGTTGTTCATGGTGAGCAAGTTGGTGAGGCAGAA
ACCATCACCAGCCATTACCTGTTTGCACTGGGTGTCTATCATACACTCTATCTCTTCAACTGGATCTGGTGTTACCACTT
CTAGGGCTTCTTTGACCTCATTGACATCCTTGCTAGCCTGATCCAGACAGTCCTCTATTGCGATTTCTTCTACCTCTATA
TCACCAAAGTCCTCAAAGGGAAGAAGCTGAACTTG

Alignment

ORF - retro_rnor_1060 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.89 %
• Parental protein coverage: 82.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SQVLF-AVVFTARYLDLFTNYISLYNTCMKVVYIACSFTTVWMIYSKFKATYDGNHD-TFRVEFLVVPTA
          SQVL....VFT..YLDLFTNYISLYNTC..VVYIACSFT.VWMIYSKFKATY.GNH..TF.VEF.VVPTA
Retrocopy SQVLL<TMVFTT*YLDLFTNYISLYNTCINVVYIACSFTIVWMIYSKFKATYGGNHE<TFQVEFFVVPTA

Parental  VLAFLVN-HDFTPLEILWTFSIYLESVAILPQLFMVSK-TGEAETITSHYLFALGVYRTLYLFNWIWRYH
          .L.F....H.FTPLEILWTFS...ESV.ILP.LFMVSK..GEAETITSHYLFALGVY.TLYLFNWIW.YH
Retrocopy ILTFKNS<HYFTPLEILWTFS--MESVTILPRLFMVSK<VGEAETITSHYLFALGVYHTLYLFNWIWCYH

Parental  FEGFFDLIAIVAGLVQTVLYCDFFYLYITKVLKGKKLSL
          F.GFFDLI.I.A.L.QTVLYCDFFYLYITKVLKGKKL.L
Retrocopy F*GFFDLIDILASLIQTVLYCDFFYLYITKVLKGKKLNL

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	48.60 RPM
SRP017611_kidney	0.00 RPM	95.46 RPM
SRP017611_liver	0.00 RPM	67.37 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1060 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1060 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1060 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000009868	1 retrocopy	retro_meug_1084,
Rattus norvegicus	ENSRNOG00000021082	1 retrocopy	retro_rnor_1060 ,