RetrogeneDB ID: retro_rnor_399

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:105872446..105873508(-)
• Located in intron of: ENSRNOG00000048759

Retrocopy information

• Ensembl ID: ENSRNOG00000008046
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Tmem30a
• Ensembl ID: ENSRNOG00000010895
• Aliases: None
• Description: Cell cycle control protein 50A [Source:UniProtKB/Swiss-Prot;Acc:Q6AY41]

Sequence

>retro_rnor_399
ATGACCTGGAGCGCCTCGGCGCGGGGCGCGCAGCAGCCCGACAACACCGCCTTCACGCAGCAGCGCCTCCCCGCCTGGCA
GCCGCTGCTGTCGGCCGGCATCACGCTGCCGCTCTTCTTCTGCGCCGGCCTGGCGTTCATCGGCCTGGGACTGGGCCTCT
TCTACTCCTCCAACGGCATCCAGGAGCTGGAGTACGACTACACCGGCAACCCCGGCACCGGCAACTGCTCGGTGTGCGCC
GCCAAGGGCCAGGACCGCGCGCCGCCGCCCAGCTGCCAGTGCTCCTGGAGCTTCACGCTGCCCGAGCTCTTCCCGGGCCC
CGTGTACCTCTACTACGAGCTGTCCAACTTTTACCAGAACAACCGGCGCTACGGCGTGTCCCGCGACGACGCTCAGCTCA
GCGGCCTGGCCAGCGCGCTGCGCCACCCGGCCAACGAGTGCGCCCCCTACCAGTTCAGCTCCGACGGCCTGCCCATCGCG
CCGTGCGGCGCCATTGCCAACAGCCTCTTCAACGATTCCTTCTCGCTCTGGCACCAGCGCCAGCCCGCGGACCCTTTCGT
CGAGGTGCCGCTCGACCGCACCGCCATCGCCTGGTGGACTGACTACCACGTCAAGTTCCGCAACCCGCCGCTGGTGAACG
GCAGCCTGGCGCTGGCCTTCAAGGGCACGGCGCCGCCGCCCAACTGGCACCGGCCGGTTTATGAGCTCAGCCCGGATCCC
AACAACACCGGCTTCATCAACCAGGACTTCGTGGTGTGGATGCGCACCGCAGCGCTGCCCACGTTCCGCAAGCTGTATGC
GCGCATCCGCCAGGGCAACTACTCGGCCGGTCTTCCCCGGGGCACTTACCGGGTCAACATCACCTACAACTACCCCGTGC
GCGCCTTCGGCGGCCACAAGCTTATCATCCTTAGCAACATCTCATGGATGGGTGGCAAGAACCCTTTTCTGGGCATCGCC
TACCTGGTCGTCGGCTCCCTCTGTATCCTCATGGGCTTTGTCATGCTGGTCGTCTACATTCGCTACCAGGACCAGGATGA
CGACGACAATGACGATGAGTGA

Alignment

ORF - retro_rnor_399 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.37 %
• Parental protein coverage: 74.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GNVFMYYGLSNFYQNHRRYVKSRDDSQLNGDPSALLNPSKECEPYRRNEDK-PIAPCGAIANSMFNDTLE
          G.V..YY.LSNFYQN.RRY..SRDD.QL.G..SAL..P..EC.PY....D..PIAPCGAIANS.FND...
Retrocopy GPVYLYYELSNFYQNNRRYGVSRDDAQLSGLASALRHPANECAPYQFSSDGLPIAPCGAIANSLFNDSFS

Parental  LFLVANESDPKPVPILLKKKGIAWWTDKNVKFRNPP-GKDSLQEKFKDTTKPVNWHKPVYELDPDDESNN
          L.......DP..V...L....IAWWTD..VKFRNPP....SL...FK.T..P.NWH.PVYEL.PD...N.
Retrocopy LWHQRQPADPF-VEVPLDRTAIAWWTDYHVKFRNPPLVNGSLALAFKGTAPPPNWHRPVYELSPDP-NNT

Parental  GFINEDFIVWMRTAALPTFRKLYRLIERTDDLHPTLPAGQYYLNITYNYPVHFFDGRKRMILSTISWMGG
          GFIN.DF.VWMRTAALPTFRKLY..I.R.......LP.G.Y..NITYNYPV..F.G.K..ILS.ISWMGG
Retrocopy GFINQDFVVWMRTAALPTFRKLYARI-RQGNYSAGLPRGTYRVNITYNYPVRAFGGHKLIILSNISWMGG

Parental  KNPFLGIAYITIGSISFLLGVVLLVINHKYRNSSN
          KNPFLGIAY...GS...L.G.V.LV....Y.....
Retrocopy KNPFLGIAYLVVGSLCILMGFVMLVVYIRYQDQDD

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	0.22 RPM	138.33 RPM
SRP017611_kidney	9.14 RPM	101.11 RPM
SRP017611_liver	0.61 RPM	95.61 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_399 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_399 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005100	1 retrocopy	retro_btau_72,
Canis familiaris	ENSCAFG00000002708	1 retrocopy	retro_cfam_26,
Callithrix jacchus	ENSCJAG00000010325	1 retrocopy	retro_cjac_801,
Cavia porcellus	ENSCPOG00000020712	1 retrocopy	retro_cpor_23,
Homo sapiens	ENSG00000112697	1 retrocopy	retro_hsap_12,
Myotis lucifugus	ENSMLUG00000011923	1 retrocopy	retro_mluc_1871,
Monodelphis domestica	ENSMODG00000018502	1 retrocopy	retro_mdom_287,
Mus musculus	ENSMUSG00000032328	1 retrocopy	retro_mmus_108,
Nomascus leucogenys	ENSNLEG00000004962	1 retrocopy	retro_nleu_69,
Otolemur garnettii	ENSOGAG00000015718	1 retrocopy	retro_ogar_22,
Pongo abelii	ENSPPYG00000016782	1 retrocopy	retro_pabe_204,
Pelodiscus sinensis	ENSPSIG00000007174	1 retrocopy	retro_psin_61,
Rattus norvegicus	ENSRNOG00000010895	1 retrocopy	retro_rnor_399 ,
Ictidomys tridecemlineatus	ENSSTOG00000002543	1 retrocopy	retro_itri_50,
Tarsius syrichta	ENSTSYG00000008211	1 retrocopy	retro_tsyr_928,