RetrogeneDB ID: retro_rnor_1829

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:138396040..138396706(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Mrpl47
• Ensembl ID: ENSRNOG00000011639
• Aliases: None
• Description: 39S ribosomal protein L47, mitochondrial [Source:RefSeq peptide;Acc:NP_001032260]

Sequence

>retro_rnor_1829
ATCTCTACCACCAGCCTAGTGAGTGTTTGCACAAGACCCTCAGCATCCCTGAAATCTTCTGGTTCCCTAGTAAGTCCCAA
GGCCCCTGCTCACTCCAGTTGCAGGTTTCTTTCAATTCATTTCATAAGAACACATCACATGCCACATCTTTTCTCCAGTG
TAAATTACTTTATACTACTTTGTCAAGGAAAGGACTAGAAGAATATTTTGATGACCCAAAGAATTGGTGAAGAGAAATCA
AATCTGGATCTTCATAGATTTGCCAGCAGCTCAGTAACAAAAATGAAGAAGACTTCTATAAACTTTTGCATGTTCTTCTG
AAGGAAAGAAACATGCTTCTAACTCTAGAGAAGGAGGCCAAATGACAGAGATAGCAAATGTCAAGTCCAGAGCGGTTAGA
AAAGGCTGTTGATTCCATGGACGCCTTAGATAAAGTTGTCCAGGAGAGGAAAGATGCTTTAAGGCTTCTTCAGATGGATC
AAGAAAAAAACAAGACTTGGTGCTTGGAGAAGGGACATCGTTGGATGAGTCATCTGGCACAAATATAAGCAGTGGCCTAT
ACCTTGGTAACCAAACAAAAGATACAACAGGAGGTAGTTTTTTGCCATACCCTATGTGGATCTCTTTATCAGACTGAGAG
TTGAGAAATACACCTGCATTGAGGCA

Alignment

ORF - retro_rnor_1829 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.22 %
• Parental protein coverage: 88.49 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAATSLVGICRRASAFLKAACSLVNPKTPAHSGCR-PPLSLLHKNTPHATSFLQCKFLHTTLSRKGLEEF
          ...TSLV..C.R.SA.LK...SLV.PK.PAHS.CR.......HKNT.HATSFLQCK.L.TTLSRKGLEE.
Retrocopy ISTTSLVSVCTRPSASLKSSGSLVSPKAPAHSSCR<VSFNSFHKNTSHATSFLQCKLLYTTLSRKGLEEY

Parental  FDDPKNWGEEKVKSGASWTCQQLRNKSNEDLHKLWYVLLKERNMLLTLEQEAKRQRLPMPSPERLEKVVD
          FDDPKNW..E..KSG.S..CQQL.NK..ED..KL..VLLKERNMLLTLE.EAK.QR..M.SPERLEK.VD
Retrocopy FDDPKNW*RE-IKSGSS*ICQQLSNKNEEDFYKLLHVLLKERNMLLTLEKEAK*QR*QMSSPERLEKAVD

Parental  SMDALDKVVQEREDALRLLQTGQE-KPRPGAWRQDIFGRIVWHKFKQWPIPWYLNKRYNRRRFFAMPYVD
          SMDALDKVVQER.DALRLLQ..QE.K.R.GAWR.DI.G...WHK.KQWPIPW..NKRYNRR.FFA.PYVD
Retrocopy SMDALDKVVQERKDALRLLQMDQE>KTRLGAWRRDIVG*VIWHKYKQWPIPW*PNKRYNRR*FFAIPYVD

Parental  SFIRLRIEKHARTEA
          .FIRLR.EK....EA
Retrocopy LFIRLRVEKYTCIEA

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	10.14 RPM
SRP017611_kidney	0.00 RPM	16.05 RPM
SRP017611_liver	0.00 RPM	4.77 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1829 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1829 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1829 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_1976

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011380	1 retrocopy	retro_cfam_1085,
Cavia porcellus	ENSCPOG00000002312	2 retrocopies	retro_cpor_1219, retro_cpor_885,
Felis catus	ENSFCAG00000031548	1 retrocopy	retro_fcat_235,
Macropus eugenii	ENSMEUG00000012649	2 retrocopies	retro_meug_1039, retro_meug_146,
Monodelphis domestica	ENSMODG00000021301	3 retrocopies	retro_mdom_1361, retro_mdom_1879, retro_mdom_562,
Mustela putorius furo	ENSMPUG00000017214	1 retrocopy	retro_mputfur_495,
Mus musculus	ENSMUSG00000037531	3 retrocopies	retro_mmus_1976, retro_mmus_1986, retro_mmus_2753,
Otolemur garnettii	ENSOGAG00000016957	2 retrocopies	retro_ogar_1900, retro_ogar_3015,
Pteropus vampyrus	ENSPVAG00000004284	1 retrocopy	retro_pvam_150,
Rattus norvegicus	ENSRNOG00000011639	2 retrocopies	retro_rnor_1829 , retro_rnor_2523,
Sorex araneus	ENSSARG00000006898	2 retrocopies	retro_sara_269, retro_sara_721,
Tursiops truncatus	ENSTTRG00000008909	1 retrocopy	retro_ttru_420,