RetrogeneDB ID: retro_rnor_1332

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:17691119..17691974(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lap3
• Ensembl ID: ENSRNOG00000003289
• Aliases: Lap3, LAP-3
• Description: Cytosol aminopeptidase [Source:UniProtKB/Swiss-Prot;Acc:Q68FS4]

Sequence

>retro_rnor_1332
CTCCAAAGTGCCAGTAGTAAAACAGAGGTCCATATCAGACCCAAATCCTGGATAAAGGAACAAGAAATGGGTTCATTCCT
AAGTGTAGCCAAGGGGTCTGAAGAGCCACCAGTGTTCTTGGAAATCCACTACGCAGGCAGCCCCAAGGCAACTGAAGCGC
CCATAGTGTTTGTGGGAAAGGGCATTACCTTTGACAGTGGAGGTCTCTCCATCAAGGCTTCTGCAAATATGGACCTCATG
AGGGCTGAGATAGGAGGAGCGGCAACAATATGCTCGACCATCGTGTCTGCAGCAAAGCTCCATTTGCCCATTAATAGCAT
AGGTTTGGTGCCTCTTTGTGAAAATATGCCTAGCGGAAAGGCCAACAAACCCGGGGATGTTGTCAGAGGCAGGAATGGGA
AGACTATCCAGGTTGACAACACTGACGCCGAGGGCAGGCTCATCCTGGCCGATGCACTCCCTTATGCACACACCTTCAAT
CCCAAGGTCATCATCAATGCTGCCACTTTAACAGGTGCGGTGGGCATAGCCCTGGGATCAGGGGCCACTGGAGTCTTTAC
CAATTCACCCTGGCTGTGGAACAAACTTTATGAGGCCAGTGTAGAAACTGGGGACCGAGTCTGGAGGATGCCCCTCTTTG
AGCATCATACCAGACAAGTCATAGATTGCCAGCTTGCTGATGCAAACGATCTTGGAAGATACAGATCTGCGGGTGCATGT
ACAGCTGTTGCATTCCTGCAAGAGTTGGTGACTCATACGAAGTGGGCACATTTAGACATAGCAGGTGTGATGACCAACAA
AGATGAGGTTCCCGATCTGGGGAAGGGAATGAGTGGGAGACCCACAAGGACTCTG

Alignment

ORF - retro_rnor_1332 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.47 %
• Parental protein coverage: 54.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKSASSKTEVHIRTKSWIEEQEMGSFLSVAKGSEEPPVFLEIHYTGSPNATEAPLVFVGKGITFDSGGIS
          L.SASSKTEVHIR.KSWI.EQEMGSFLSVAKGSEEPPVFLEIHY.GSP.ATEAP.VFVGKGITFDSGG.S
Retrocopy LQSASSKTEVHIRPKSWIKEQEMGSFLSVAKGSEEPPVFLEIHYAGSPKATEAPIVFVGKGITFDSGGLS

Parental  IKASANMDLMRADMGGAATICSAIVSAAKLNLPINIIGLAPLCENMPSGKANKPGDVVRARNGKTIQVDN
          IKASANMDLMRA..GGAATICS.IVSAAKL.LPIN.IGL.PLCENMPSGKANKPGDVVR.RNGKTIQVDN
Retrocopy IKASANMDLMRAEIGGAATICSTIVSAAKLHLPINSIGLVPLCENMPSGKANKPGDVVRGRNGKTIQVDN

Parental  TDAEGRLILADALCYAHTFNPKVIINAATLTGAMDVALGSGATGVFTNSSWLWNKLFEASVETGDRVWRM
          TDAEGRLILADAL.YAHTFNPKVIINAATLTGA...ALGSGATGVFTNS.WLWNKL.EASVETGDRVWRM
Retrocopy TDAEGRLILADALPYAHTFNPKVIINAATLTGAVGIALGSGATGVFTNSPWLWNKLYEASVETGDRVWRM

Parental  PLFEHYTRQVIDCQLADVNNLGKYRSAGACTAAAFLREFVTHTKWAHLDIAGVMTNKDEIPYLRKGMSGR
          PLFEH.TRQVIDCQLAD.N.LG.YRSAGACTA.AFL.E.VTHTKWAHLDIAGVMTNKDE.P.L.KGMSGR
Retrocopy PLFEHHTRQVIDCQLADANDLGRYRSAGACTAVAFLQELVTHTKWAHLDIAGVMTNKDEVPDLGKGMSGR

Parental  PTRTL
          PTRTL
Retrocopy PTRTL

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	36.24 RPM
SRP017611_kidney	0.00 RPM	183.53 RPM
SRP017611_liver	0.00 RPM	229.62 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1332 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1332 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1332 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000004383	1 retrocopy	retro_cint_4,
Homo sapiens	ENSG00000002549	1 retrocopy	retro_hsap_3457,
Gorilla gorilla	ENSGGOG00000001110	1 retrocopy	retro_ggor_2333,
Nomascus leucogenys	ENSNLEG00000016606	1 retrocopy	retro_nleu_2711,
Pongo abelii	ENSPPYG00000014626	1 retrocopy	retro_pabe_2858,
Pan troglodytes	ENSPTRG00000015938	1 retrocopy	retro_ptro_2344,
Rattus norvegicus	ENSRNOG00000003289	1 retrocopy	retro_rnor_1332 ,
Tursiops truncatus	ENSTTRG00000006175	1 retrocopy	retro_ttru_1013,