RetrogeneDB ID: retro_rnor_331

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 19:36367928..36369101(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000008450
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RRM2
• Ensembl ID: ENSRNOG00000023272
• Aliases: None
• Description: Ribonucleoside-diphosphate reductase subunit M2 [Source:UniProtKB/Swiss-Prot;Acc:Q4KLN6]

Sequence

>retro_rnor_331
ATGCTCTCGGTCCGCGCCCCGCTCGCCACCATCGCTGACCAGCAGCAGCTGCACTTGTCGCCCCTGAAGCGACTCAGTCT
GGCTGACAAGGAGAACACGCCCCCAACCCTCAGCAGCGCCCGCGTCCTGGCTAGCAAGGCTGCAAGGAGAATCTTCCAGG
ACTCTGCCGAGCTGGAAAGTAAAGCACCCACTAAACCCAGCATTGAGGAAGAGCCGTTACTGAGAGAAAATCCCCGCCGT
TTCGTTGTCTTTCCCATCGAATACCATGATATCTGGCAGATGTACAAGAAAGCTGAGGCCTCCTTTTGGACTGCCGAGGA
GGTGGACCTTTCCAAGGATATTCAGCACTGGGAAGCTCTGAAACCAGATGAGAGACATTTTATATCTCATGTTCTGGCCT
TCTTTGCGGCGAGTGATGGCATAGTCAATGAGAACTTGGTGGAGCGATTTAGCCAAGAAGTTCAAGTCACAGAGGCCCGC
TGTTTCTATGGCTTCCAAATTGCCATGGAGAACATACACTCCGAAATGTACAGTCTCCTTATTGACACTTACATTAAAGA
TTCCAAAGAAAGAGAATATCTCTTCAACGCCATTGAGACAATGCCTTGTGTGAAGAAGAAGGCTGACTGGGCCTTGCGTT
GGATTGGGGACAAAGAGGCTACGTATGGAGAACGAGTTGTGGCCTTCGCTGCGGTAGAAGGAATCTTCTTTTCTGGTTCT
TTTGCATCAATATTCTGGCTCAAGAAACGGGGACTGATGCCGGGCCTTACATTTTCCAATGAACTTATTAGCAGAGATGA
GGGTCTGCACTGTGACTTTGCCTGCCTGATGTTCAAGCACCTGGTACACAAGCCCTCGGAGCAGAGAGTAAAAGAAATAA
TTACCAACGCGGTCAGGATAGAGCAGGAGTTCCTCACAGAGGCCCTGCCTGTGAAGCTCATCGGGATGAATTGCACCTTG
ATGAAGCAGTACATCGAGTTTGTGGCCGACAGGCTTATGCTGGAGCTGGGTTTTAACAAGATTTTCAAAGTAGAAAATCC
ATTTGACTTCATGGAGAATATTTCACTAGAAGGAAAAACAAACTTCTTTGAGAAGCGAGTAGGCGAGTACCAGAGGATGG
GAGTAATGTCAAATTCGACAGAAAATTCTTTCACCTTGGATGCTGACTTCTAA

Alignment

ORF - retro_rnor_331 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSVRAPLATIADQQQLHLSPLKRLSLADKENTPPTLSSARVLASKAARRIFQDSAELESKAPTKPSIEE
          MLSVRAPLATIADQQQLHLSPLKRLSLADKENTPPTLSSARVLASKAARRIFQDSAELESKAPTKPSIEE
Retrocopy MLSVRAPLATIADQQQLHLSPLKRLSLADKENTPPTLSSARVLASKAARRIFQDSAELESKAPTKPSIEE

Parental  EPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPDERHFISHVLAFFAASDG
          EPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPDERHFISHVLAFFAASDG
Retrocopy EPLLRENPRRFVVFPIEYHDIWQMYKKAEASFWTAEEVDLSKDIQHWEALKPDERHFISHVLAFFAASDG

Parental  IVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDSKEREYLFNAIETMPCVKKKADW
          IVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDSKEREYLFNAIETMPCVKKKADW
Retrocopy IVNENLVERFSQEVQVTEARCFYGFQIAMENIHSEMYSLLIDTYIKDSKEREYLFNAIETMPCVKKKADW

Parental  ALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKH
          ALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKH
Retrocopy ALRWIGDKEATYGERVVAFAAVEGIFFSGSFASIFWLKKRGLMPGLTFSNELISRDEGLHCDFACLMFKH

Parental  LVHKPSEQRVKEIITNSVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFKVENPFDF
          LVHKPSEQRVKEIITN.VRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFKVENPFDF
Retrocopy LVHKPSEQRVKEIITNAVRIEQEFLTEALPVKLIGMNCTLMKQYIEFVADRLMLELGFNKIFKVENPFDF

Parental  MENISLEGKTNFFEKRVGEYQRMGVMSNSTENSFTLDADF
          MENISLEGKTNFFEKRVGEYQRMGVMSNSTENSFTLDADF
Retrocopy MENISLEGKTNFFEKRVGEYQRMGVMSNSTENSFTLDADF

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	0.79 RPM
SRP017611_kidney	0.00 RPM	1.88 RPM
SRP017611_liver	0.00 RPM	1.21 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

4 EST(s) were mapped to retro_rnor_331 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DW370457	36368752	36368897	97	130	2	125
DW370667	36368770	36368897	99.3	126	1	125
DW377111	36368770	36368897	97.7	124	3	121
DW395596	36368770	36368900	100	130	0	130

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_331 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_331 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003409	1 retrocopy	retro_cfam_2113,
Callithrix jacchus	ENSCJAG00000006533	3 retrocopies	retro_cjac_2134, retro_cjac_2950, retro_cjac_3851,
Cavia porcellus	ENSCPOG00000008652	1 retrocopy	retro_cpor_8,
Erinaceus europaeus	ENSEEUG00000009755	2 retrocopies	retro_eeur_421, retro_eeur_585,
Echinops telfairi	ENSETEG00000015797	2 retrocopies	retro_etel_640, retro_etel_691,
Homo sapiens	ENSG00000171848	1 retrocopy	retro_hsap_4815,
Macropus eugenii	ENSMEUG00000000121	3 retrocopies	retro_meug_1450, retro_meug_199, retro_meug_277,
Microcebus murinus	ENSMICG00000012789	1 retrocopy	retro_mmur_1384,
Myotis lucifugus	ENSMLUG00000010596	1 retrocopy	retro_mluc_794,
Macaca mulatta	ENSMMUG00000002057	1 retrocopy	retro_mmul_2568,
Monodelphis domestica	ENSMODG00000014763	1 retrocopy	retro_mdom_775,
Mus musculus	ENSMUSG00000020649	2 retrocopies	retro_mmus_2472, retro_mmus_3073,
Nomascus leucogenys	ENSNLEG00000013733	2 retrocopies	retro_nleu_2190, retro_nleu_3040,
Otolemur garnettii	ENSOGAG00000007075	1 retrocopy	retro_ogar_2665,
Pongo abelii	ENSPPYG00000012656	1 retrocopy	retro_pabe_3743,
Rattus norvegicus	ENSRNOG00000023272	1 retrocopy	retro_rnor_331 ,
Sus scrofa	ENSSSCG00000021742	1 retrocopy	retro_sscr_901,
Tursiops truncatus	ENSTTRG00000017209	1 retrocopy	retro_ttru_603,