RetrogeneDB ID: retro_rnor_629

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:205732326..205732763(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufa13
• Ensembl ID: ENSRNOG00000020602
• Aliases: None
• Description: None

Sequence

>retro_rnor_629
ATGTCGGCGTCGAAGGTGAAGCAGGACATGCCCCCACCAGGGGGCTACAGCCCCATCGATTACAAGCGGAACCTGCCCTG
CTGGGGACTGTCGGGATACAGCATGTTTGCTTTGGGCATCGGGGCCTTGATCTTTGGCTACTGGAGAATAATGAGGTGGA
ACCAGGAGTGTAGGCACCTGCTGATCGAGGACTTGGAGGCCAGGATCGCCCTCATGCCACTCCTCCAGGCAGAGAAGACC
GCAGGACCCTGCAGATTCTTCGGGAGAATCTGGAGGAGGAGGCCATCATCATGAAAGATGTGCCCAACTGGAAGGTGGGG
GAGTCTATGTTCCATACCACACGATGGGTGCCACCCCTCATCGGCGAGCTTTATGGGTTACGCACCAAGGAGGAGATGGA
GAACACGAACACCAACTTCGGCTTCACCGGGTACACT

Alignment

ORF - retro_rnor_629 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.52 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAASKVKQDMPPPGGYGPIDYKRNLPRRGLSGYSMFALGIGALIFGYWRIMRWNRERRRLLIEDLEARIA
          M.ASKVKQDMPPPGGY.PIDYKRNLP..GLSGYSMFALGIGALIFGYWRIMRWN.E.R.LLIEDLEARIA
Retrocopy MSASKVKQDMPPPGGYSPIDYKRNLPCWGLSGYSMFALGIGALIFGYWRIMRWNQECRHLLIEDLEARIA

Parental  LMPLLQAEK-DRRTLQILRENLEEEAIIMKDVPNWKVGESMFHTTRWVPPLIGELYGLRTKEEME--NAN
          LMPLLQAEK.DRRTLQILRENLEEEAIIMKDVPNWKVGESMFHTTRWVPPLIGELYGLRTKEEME..N.N
Retrocopy LMPLLQAEK<DRRTLQILRENLEEEAIIMKDVPNWKVGESMFHTTRWVPPLIGELYGLRTKEEMENTNTN

Parental  FGFTGYT
          FGFTGYT
Retrocopy FGFTGYT

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	28.11 RPM
SRP017611_kidney	0.07 RPM	46.96 RPM
SRP017611_liver	1.21 RPM	31.80 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_629 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_629 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_629 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034503	1 retrocopy	retro_cjac_262,
Mus musculus	ENSMUSG00000036199	1 retrocopy	retro_mmus_2453,
Rattus norvegicus	ENSRNOG00000020602	2 retrocopies	retro_rnor_210, retro_rnor_629 ,
Sorex araneus	ENSSARG00000004735	1 retrocopy	retro_sara_693,
Sus scrofa	ENSSSCG00000013936	3 retrocopies	retro_sscr_707, retro_sscr_722, retro_sscr_739,
Tursiops truncatus	ENSTTRG00000009880	1 retrocopy	retro_ttru_1141,