RetrogeneDB ID: retro_rnor_1979

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:142599906..142600433(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl17
• Ensembl ID: ENSRNOG00000019497
• Aliases: None
• Description: 39S ribosomal protein L17, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q6PDW6]

Sequence

>retro_rnor_1979
ATGAGGTTGTCCCTAGCTGCCACTATCTCCCATGGCCGCGTCTACCGCTGCCTGGGCCTCGGTCCCGAGTCCCGGATCCA
CCTGCTACGGAACTTGCTCACAGGCCTAGTTCACCACGAACGCATCGAGGCGACTTAGGCACGCATGGACGAGATGAGGG
GCTACACGGAGAAGCTCATTGACTATGGAAAGCTGGGAGACACCAACAATGAGCCATGCGTATGGCTGACTTCTGGCTCA
CTGAGAAGGACTTGATCCCAAAGCAGTTTAAAGTGTTAGCGCCTCCGTTCCAAGGTCAGAATGGCAACTACACAAGAATG
CTACAGATCCCGAATCGAAAGGAACAAGATCGGGCCAAGATGGCAGTGATAGACTATAAGGGGAACTGCCTCCCTCCCCT
GTCTCTGCCTCACAGAGATAGCAACCTTACTATCCTAAACCAGCTACTCCTGGGACTGCAGCAGGACCTGCACCACAACC
AGGAAGCAAGCCTCCACAGCTCCCATACGGTTTAAACACCAAAGACT

Alignment

ORF - retro_rnor_1979 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRLSLAAAISHGRVYRRLGLGPESRIHLLRNLLTGLVRHERIEATWARVDEMRGYAEKLIDYGKLGDTNE
          MRLSLAA.ISHGRVYR.LGLGPESRIHLLRNLLTGLV.HERIEAT.AR.DEMRGY.EKLIDYGKLGDTN.
Retrocopy MRLSLAATISHGRVYRCLGLGPESRIHLLRNLLTGLVHHERIEAT*ARMDEMRGYTEKLIDYGKLGDTNN

Parental  R-AMRMADFWLTEKDLIPKLFKVLAPRFQGQNGNYTRMLQIPNRKEQDRAKMAVIEYKGNCLPPLPLPHR
          ..AMRMADFWLTEKDLIPK.FKVLAP.FQGQNGNYTRMLQIPNRKEQDRAKMAVI.YKGNCLPPL.LPHR
Retrocopy E<AMRMADFWLTEKDLIPKQFKVLAPPFQGQNGNYTRMLQIPNRKEQDRAKMAVIDYKGNCLPPLSLPHR

Parental  DSNLTLLNQLLLGLQQDLHHNQKASLHSSHTVQTPKT
          DSNLT.LNQLLLGLQQDLHHNQ.ASLHSSHTV.TPKT
Retrocopy DSNLTILNQLLLGLQQDLHHNQEASLHSSHTV*TPKT

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	47.52 RPM
SRP017611_kidney	0.00 RPM	54.99 RPM
SRP017611_liver	0.00 RPM	37.32 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1979 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1979 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1979 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
Cavia porcellus	ENSCPOG00000027536	1 retrocopy	retro_cpor_1430,
Macropus eugenii	ENSMEUG00000013588	1 retrocopy	retro_meug_1822,
Myotis lucifugus	ENSMLUG00000001144	2 retrocopies	retro_mluc_2368, retro_mluc_679,
Mustela putorius furo	ENSMPUG00000005449	1 retrocopy	retro_mputfur_125,
Rattus norvegicus	ENSRNOG00000019497	1 retrocopy	retro_rnor_1979 ,
Sus scrofa	ENSSSCG00000024693	1 retrocopy	retro_sscr_217,
Ictidomys tridecemlineatus	ENSSTOG00000003313	3 retrocopies	retro_itri_1019, retro_itri_1156, retro_itri_240,