RetrogeneDB ID: retro_rnor_73

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:123480732..123481290(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000013038
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rab5c
• Ensembl ID: ENSRNOG00000018568
• Aliases: None
• Description: ras-related protein Rab-5C [Source:RefSeq peptide;Acc:NP_001099310]

Sequence

>retro_rnor_73
CGGGTGGAGGAGGTGCAAGCACGACCCAATGGACCAGCTGCAGGCAACAAGATCTGTCAGTTTAAGCTGATCCTCTTGGG
CGAGTCTGCAATGGGCAAATCCAGCCTGGTCCTCCGCTTTGTCAAGTGGCAGTTCCACGAGTACCAGGAGAGCACAATTG
GAGCGGCTTTCCTCACACAGACTGTCTGCGTAGATGACACAAGGGTCAAGTTTGAGATCTGGGACACAGCTGGGCGAGAG
CGATATCACAGCCTGTCCCCGATGTACTATCGGGGGGTGGGGGGGGGGCAAGCAGCCATTGTGGTCTATGACTTCACCAA
CACAGATACATTTGCACGGGCTAAGAATTGGGTGAAGGAGTTACAGAGGCAAGCCAGCTCCAACATCGTCATTGCACTAG
CGGGTAACAAAGCAGACCTGGCCAGCAAGAGAGCCATGGAGTTTCAGGAAGCACAAGCCTACGCAGATGACAACAGTTTG
CTGTTCATGGAGACGTCCGCGAAGACTGCAATGAATGTGAATGAAATTTTCATGGCAATAGCCAGGTGGTCGGGTCTC

Alignment

ORF - retro_rnor_73 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.48 %
• Parental protein coverage: 80.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ARPNGPAAGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTVKFEIWDT
          ARPNGPAAGNKICQFKL.LLGESA.GKSSLVLRFVK.QFHEYQESTIGAAFLTQTVC.DDT.VKFEIWDT
Retrocopy ARPNGPAAGNKICQFKLILLGESAMGKSSLVLRFVKWQFHEYQESTIGAAFLTQTVCVDDTRVKFEIWDT

Parental  AGQERYHSLAPMYYRG---AQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADLASKRAV
          AG.ERYHSL.PMYYRG....QAAIVVYD.TNTDTFARAKNWVKELQRQAS.NIVIALAGNKADLASKRA.
Retrocopy AGRERYHSLSPMYYRGVGGGQAAIVVYDFTNTDTFARAKNWVKELQRQASSNIVIALAGNKADLASKRAM

Parental  EFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAK
          EFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIA.
Retrocopy EFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAR

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	92.39 RPM
SRP017611_kidney	0.14 RPM	157.71 RPM
SRP017611_liver	0.13 RPM	54.33 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_73 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_73 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_73 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Cavia porcellus	ENSCPOG00000011190	2 retrocopies	retro_cpor_333, retro_cpor_473,
Dipodomys ordii	ENSDORG00000006819	1 retrocopy	retro_dord_428,
Macropus eugenii	ENSMEUG00000005614	1 retrocopy	retro_meug_2118,
Monodelphis domestica	ENSMODG00000014792	1 retrocopy	retro_mdom_1399,
Pongo abelii	ENSPPYG00000008398	1 retrocopy	retro_pabe_2664,
Rattus norvegicus	ENSRNOG00000018568	2 retrocopies	retro_rnor_393, retro_rnor_73 ,