RetrogeneDB ID: retro_rnor_823

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 11:10726943..10727463(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kdelc1
• Ensembl ID: ENSRNOG00000011740
• Aliases: None
• Description: KDEL motif-containing protein 1 precursor [Source:RefSeq peptide;Acc:NP_001101687]

Sequence

>retro_rnor_823
AAAAATCTGAAGTTAGAGGTTAAACACCTCAGGCAACATGTGGCCAAGTCTCCTTATGTTTCAAGAGGACCGGTTTACCG
TGAGAACTGTGGTTGCCCTTTGGATGACAGTGCAGCCTGGCTACGGGAGATGAATTGTTCAGAAACTGAAACTCAGATTC
AGAAAGATCTGTCACATTTCCCTACTGTCGATTCTGAAAAGATTGCAGCAGAAACCCAAAACGATCTGGACAGAGGCAAA
GCCTGTGTCACTATACCTTAAAGGACAATAAGGTCCACGTTGAGACTCATGGTGAGCATGTTGGCTTTAGGATTTTCACA
GATGCAATACTACTTTCATTGACTAGAAAGGCGAGGATGCCAGATGTGGAATTTTTTGTTAACTTGGGAGAGTGACCTTG
GGAAAAAGGAAATCCAACTTCAAGATTCAACCAATCTTTTCCTGTTGTGGCTCCACAGAGTCCAGGGTTATTGTGATGCC
TACGTATGACCTGACTGACTCTATTCTAGAAACCATGGGC

Alignment

ORF - retro_rnor_823 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 61.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RNLKIEVKHHGQHVAKSPYILRGPVYHENCDCPLEDSAAWLREMNCPETITQIQKDLSHFPTVDPEKIAA
          .NLK.EVKH..QHVAKSPY..RGPVY.ENC.CPL.DSAAWLREMNC.ET.TQIQKDLSHFPTVD.EKIAA
Retrocopy KNLKLEVKHLRQHVAKSPYVSRGPVYRENCGCPLDDSAAWLREMNCSETETQIQKDLSHFPTVDSEKIAA

Parental  EI-PKRFGQRQSLCHYTLKDNKVYIKTHGEHVGFRIFMDAILLSLTRKVRMPEVEFFVNLGDWPLE-KKK
          E..PKR.GQRQSLCHYTLKDNKV...THGEHVGFRIF.DAILLSLTRK.RMP.VEFFVNLG..P.E.K.K
Retrocopy ET<PKRSGQRQSLCHYTLKDNKVHVETHGEHVGFRIFTDAILLSLTRKARMPDVEFFVNLGE*PWE<KRK

Parental  STSNIQPIFSWCGSTESRDIVMPTYDLTDSVLETMG
          S...IQPIFS.CGSTESR.IVMPTYDLTDS.LETMG
Retrocopy SNFKIQPIFSCCGSTESRVIVMPTYDLTDSILETMG

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	12.01 RPM
SRP017611_kidney	0.00 RPM	10.61 RPM
SRP017611_liver	0.00 RPM	8.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_823 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_823 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_823 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000007858	1 retrocopy	retro_nleu_954,
Pongo abelii	ENSPPYG00000005483	1 retrocopy	retro_pabe_2683,
Rattus norvegicus	ENSRNOG00000011740	1 retrocopy	retro_rnor_823 ,