RetrogeneDB ID: retro_rnor_393

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:72908161..72908809(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000005028
• 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_393
ATGGCTAATCGAGGAGCAACAAGACCCAACGGGCCAAATACTGGAAATAAAATATGCCAGTTCAAACTGGTACTTCTAGG
AGAGTCTGCTGTTGGCAAATCAAGTCTGGTGCTTCGCTTTGTGAAAGGCCAATTTCATGAGTTTCAAGAGAGTACCATTG
GGGCTGCCTTTCTAACCCAAACTGTGTGTCTTGATGACACAACAGTAAAATTTGAAATATGGGATACAGCTGGCCAAGAA
CGGTATCATAGCCTAGCACCAATGTACTACCGAGGAGCACAAGCCGCCATAGTTGTGTATGATATTACAAATGAGGAGTC
CTTTTCGAGAGCAAAAAACTGGGTTAAAGAACTTCAAAGGCAAGCGAGTCCTAATATTGTGATAGCTTTGTCAGGAAACA
AGGCTGACTTAGCAAATAAAAGAGCTGTTGACTTCCAGGAAGCACAGTCCTATGCAGATGACAACAGCTTATTATTTATG
GAGACATCAGCTAAGACACCAATGAATGTAAATGAAATATTTATGGCAATAGCTAAAAAGCTGCCAAAGAACGAACCACA
AAATCCAGGCGCAAACTCAGCCAGAGGACGAGGAGTAGACCTTACTGAGCCTGCACAGCCAGCCAGAAGCCAGTGTTGTA
GTAACTGA

Alignment

ORF - retro_rnor_393 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.04 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGRGGAARPNGPAAGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEYQESTIGAAFLTQTVCLDDTTV
          MA.RG.A.RPNGP..GNKICQFKLVLLGESAVGKSSLVLRFVKGQFHE.QESTIGAAFLTQTVCLDDTTV
Retrocopy MANRG-ATRPNGPNTGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTV

Parental  KFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNTDTFARAKNWVKELQRQASPNIVIALAGNKADLAS
          KFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITN...F.RAKNWVKELQRQASPNIVIAL.GNKADLA.
Retrocopy KFEIWDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFSRAKNWVKELQRQASPNIVIALSGNKADLAN

Parental  KRAVEFQEAQAYADDNSLLFMETSAKTAMNVNEIFMAIAKKLPKNEPQNAAGAPGRNRGVDLQESNPASR
          KRAV.FQEAQ.YADDNSLLFMETSAKT.MNVNEIFMAIAKKLPKNEPQN......R.RGVDL.E.....R
Retrocopy KRAVDFQEAQSYADDNSLLFMETSAKTPMNVNEIFMAIAKKLPKNEPQNPGANSARGRGVDLTEPAQPAR

Parental  SQCCSN
          SQCCSN
Retrocopy SQCCSN

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	28.11 RPM	92.39 RPM
SRP017611_kidney	21.21 RPM	157.71 RPM
SRP017611_liver	10.35 RPM	54.33 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_rnor_393 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CB813196	72908125	72908482	99.5	355	1	352

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_393 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_393 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,