RetrogeneDB ID: retro_rnor_644

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:236361479..236362632(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Larp4
• Ensembl ID: ENSRNOG00000049091
• Aliases: None
• Description: La ribonucleoprotein domain family, member 4 [Source:MGI Symbol;Acc:MGI:2443114]

Sequence

>retro_rnor_644
GGTAGCTTTGTGAATGGCTTTAGTTCACCGGGATCTTATAAAACAAATGCTGCTGCTATGAATATGGGCCGACCATTCCA
AAAAAATCGTGTGAAGCCTCATTTTAGGTCATCTAGTGGTTCAGAACACTCAACAGATGGATCTGTGTCATTGGGGGATG
GACCGTTGAGCAGATCTAGTTCAAGGATCTTTCTTTCTGAACGGCATAACCCAACAGTAACAGGGCATCAGGAACAAACT
TATCTTCCAAAGGATGCTCCCATTTTACAGATGGAACAGAATGGGGACTTTGGAAGAGGCAGGAGAACTCTCTTTAGAGG
TTGAAGACGAAGAGAAGATGACAGGATCCCAAGACCCCAACCTGCCGCAACTGAAGCAAAGGCTCCAGCACCAAAGTTTG
ACTTACTTGCTACAAATTTCCCTCCTCTACCCGGAAGCTCATCAAGAATGCCAGATGAACTCGCTTTGGAGAAGAGAATG
TCTGATGTTGTTAAAAGTGTCTGCAAAGAAAAGGACAATGAGGACTTGAGAGTTAGTTGTCCGGTGCCTGCAGAAGACGG
ACAGACAGACTGCGCTTCTGTGCCACAACTCAGCATAAGTCCTAGTCCTCCATGTACAGCTGAGCCTCCTGCATTAAGCA
GCACAACTCAGAAGGAGAAGGATCAAATGGAGGATTCCGCTGCTCCAAAAGATGTTCTCAATCCAGTGCCAGTGCCAGTG
CCAGTGTCTTCTCCAACTACTACAAAGCCATCAAGGGCAAACACTGCTTCACCTTGCAATAGTACCGTAAATACACCTAT
AGCTGTGGCCCCACAGGAACCTCGAAAGTTAAGCTATGCTGAAGTGTGCCAGAAGCCTCCTAAGGAGCGGTCTCCGGTTC
TTGTCCAGCCACTGAGGGAGCTTCGGTCCAATGTAGAGTCTCCCACCAGAAACGAAGAGAACGGAGCTCCTGAGAAGCCT
GTTGAGAAGCCACAGGAAAAACCGGAAACAAGGGCTAGTAAGGATCATTTCTGGCTTCCGAGGCAACACCATTCCCCGAG
GAGCAGCTGGAAAAATCAGGGAACAGAGACGCCAGTTCAGCCATAGGGCTGCACCTCAGGGAGTGACTCGACAGAATGGG
AAGGAGCAGTAAGTGCCACCCAGATCACCAAAG

Alignment

ORF - retro_rnor_644 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.83 %
• Parental protein coverage: 52.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GFFVFIFKNKGSYKNNKN-YEQTRPFIKISVKPHFRSSSGSEHSTDGSVSLGDGPVSRSSSRIFLSERHN
          G.FV..F...GSYK.N.......RPF.K..VKPHFRSSSGSEHSTDGSVSLGDGP.SRSSSRIFLSERHN
Retrocopy GSFVNGFSSPGSYKTNAAAMNMGRPFQKNRVKPHFRSSSGSEHSTDGSVSLGDGPLSRSSSRIFLSERHN

Parental  PTVTGHQEQTYLPKDAPILQMEQNGDFGRGRRTLFRGRRRREDDRIPRPQPAATEAKAPAPKFDLLATNF
          PTVTGHQEQTYLPKDAPILQMEQNGDFGRGRRTLFRG.RRREDDRIPRPQPAATEAKAPAPKFDLLATNF
Retrocopy PTVTGHQEQTYLPKDAPILQMEQNGDFGRGRRTLFRG*RRREDDRIPRPQPAATEAKAPAPKFDLLATNF

Parental  PPLPGSSSRMPDELALENRMSDVVKGVCKEKDNEDLRVSCPVPAEDGQTDCASVPQLSISPSPPCTAEPP
          PPLPGSSSRMPDELALE.RMSDVVK.VCKEKDNEDLRVSCPVPAEDGQTDCASVPQLSISPSPPCTAEPP
Retrocopy PPLPGSSSRMPDELALEKRMSDVVKSVCKEKDNEDLRVSCPVPAEDGQTDCASVPQLSISPSPPCTAEPP

Parental  AL-STTQQEKDQMEDSAAPKDVLNPVPVPVSSPTTT--KPSRANTASPCNSTVNTPIAVAPQEPRKLSYA
          AL.STTQ.EKDQMEDSAAPKDVLN...........T..KPSRANTASPCNSTVNTPIAVAPQEPRKLSYA
Retrocopy ALSSTTQKEKDQMEDSAAPKDVLNXXXXXXXXSSPTTTKPSRANTASPCNSTVNTPIAVAPQEPRKLSYA

Parental  EVCQKPPKEPSPVLVQPLRELRSNVVSPTRNEENGAPEKPVEKPQEKPETRASKDH-SGFRGNTIPRGAA
          EVCQKPPKE.SPVLVQPLRELRSNV.SPTRNEENGAPEKPVEKPQEKPETRASKDH.SGFRGNTIPRGAA
Retrocopy EVCQKPPKERSPVLVQPLRELRSNVESPTRNEENGAPEKPVEKPQEKPETRASKDH>SGFRGNTIPRGAA

Parental  GKIREQRRQFSHRAAPQGVTRQNGKEQIVSRKSPK
          GKIREQRRQFSHRAAPQGVTRQNGKEQ.V...SPK
Retrocopy GKIREQRRQFSHRAAPQGVTRQNGKEQ*VPPRSPK

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	2.37 RPM	7.33 RPM
SRP017611_kidney	5.44 RPM	19.61 RPM
SRP017611_liver	3.03 RPM	13.31 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_644 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_644 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_644 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000161813	1 retrocopy	retro_hsap_1483,
Myotis lucifugus	ENSMLUG00000012513	1 retrocopy	retro_mluc_1180,
Macaca mulatta	ENSMMUG00000008172	1 retrocopy	retro_mmul_2129,
Mus musculus	ENSMUSG00000023025	1 retrocopy	retro_mmus_3568,
Nomascus leucogenys	ENSNLEG00000017798	1 retrocopy	retro_nleu_2388,
Pan troglodytes	ENSPTRG00000004935	1 retrocopy	retro_ptro_1003,
Rattus norvegicus	ENSRNOG00000049091	1 retrocopy	retro_rnor_644 ,