RetrogeneDB ID: retro_rnor_57

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:95438962..95439316(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000032756
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Gabarapl2
• Ensembl ID: ENSRNOG00000019425
• Aliases: Gabarapl2, Gef2
• Description: Gamma-aminobutyric acid receptor-associated protein-like 2 [Source:UniProtKB/Swiss-Prot;Acc:P60522]

Sequence

>retro_rnor_57
ATGAAGTGGATGTTTAAGGAGGACCACTCGCTGGAACACAGATGCGTGGAATCCGCGAAGATCAGAGCGAAATACCCCGA
CCGGGTTCCGGTGATCGTTGAGAAAGTCTCTGGCTCTCAGATTGTTGACATTGACAAGAGGAAGTACTTGGTCCCATCTG
ACATCACTGTGGCTCAGTTCATGTGGATCATCAGGAAAAGGATCCAGCTTCCTTCTGAGAAGGCCATCTTCTTGTTTGTG
GACAAGACAGTCCCACAGTCCAGCCTAACTATGGGACAGCTTTACGAGAAGGAAAAAGATGAAGATGGATTCTTGTATGT
GGCCTACAGCGGAGAGAACACTTTTGGCTTCTGA

Alignment

ORF - retro_rnor_57 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQL
          MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQL
Retrocopy MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQL

Parental  PSEKAIFLFVDKTVPQSSLTMGQLYEKEKDEDGFLYVAYSGENTFGF
          PSEKAIFLFVDKTVPQSSLTMGQLYEKEKDEDGFLYVAYSGENTFGF
Retrocopy PSEKAIFLFVDKTVPQSSLTMGQLYEKEKDEDGFLYVAYSGENTFGF

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	0.07 RPM	35.66 RPM
SRP017611_kidney	0.35 RPM	27.22 RPM
SRP017611_liver	0.00 RPM	21.99 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_57 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_57 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_57 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005453	2 retrocopies	retro_amel_1054, retro_amel_1238,
Canis familiaris	ENSCAFG00000031455	1 retrocopy	retro_cfam_639,
Callithrix jacchus	ENSCJAG00000014253	1 retrocopy	retro_cjac_146,
Dasypus novemcinctus	ENSDNOG00000002240	2 retrocopies	retro_dnov_1755, retro_dnov_2332,
Erinaceus europaeus	ENSEEUG00000011134	1 retrocopy	retro_eeur_337,
Homo sapiens	ENSG00000034713	1 retrocopy	retro_hsap_4115,
Gorilla gorilla	ENSGGOG00000012299	2 retrocopies	retro_ggor_2761, retro_ggor_342,
Loxodonta africana	ENSLAFG00000017065	2 retrocopies	retro_lafr_234, retro_lafr_543,
Microcebus murinus	ENSMICG00000011981	1 retrocopy	retro_mmur_1473,
Myotis lucifugus	ENSMLUG00000015112	1 retrocopy	retro_mluc_1207,
Macaca mulatta	ENSMMUG00000005759	2 retrocopies	retro_mmul_2369, retro_mmul_540,
Mustela putorius furo	ENSMPUG00000009894	1 retrocopy	retro_mputfur_993,
Mus musculus	ENSMUSG00000031950	5 retrocopies	retro_mmus_2637, retro_mmus_2655, retro_mmus_3240, retro_mmus_456, retro_mmus_506,
Nomascus leucogenys	ENSNLEG00000013048	2 retrocopies	retro_nleu_1560, retro_nleu_580,
Pongo abelii	ENSPPYG00000007565	2 retrocopies	retro_pabe_3368, retro_pabe_372,
Pan troglodytes	ENSPTRG00000008362	2 retrocopies	retro_ptro_250, retro_ptro_2794,
Rattus norvegicus	ENSRNOG00000017417	2 retrocopies	retro_rnor_1818, retro_rnor_2093,
Rattus norvegicus	ENSRNOG00000017905	5 retrocopies	retro_rnor_1240, retro_rnor_1739, retro_rnor_1865, retro_rnor_1868, retro_rnor_2033,
Rattus norvegicus	ENSRNOG00000019425	1 retrocopy	retro_rnor_57 ,