RetrogeneDB ID: retro_rnor_863

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 12:16140621..16142151(+)
• Located in intron of: ENSRNOG00000024456

Retrocopy information

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

Parental gene information

• Parental gene symbol: Papola
• Ensembl ID: ENSRNOG00000004827
• Aliases: None
• Description: poly(A) polymerase alpha [Source:RefSeq peptide;Acc:NP_001101526]

Sequence

>retro_rnor_863
ATGCCATTTGCGGTGACCACCCAAGGAGCACAACAACCGGCTCCCGCCCCGAAGCAGTACGGCATATCGTCCCCCATCAG
CCTGGCCGCCCCCAAGGACACAGACCGCGAACTCACCCAGAAGCTGATCGAGACCCTCCAGCCCTTCGGGGTGTTTGAAG
AGGAAGAGGAACTGCAGCGCAGGATTTTAATTTTGCAGAAATTAAATAATCTGGTGAAGGAATGGATCCGAGAAATCAGT
GAAAGCAGGAATCTTCCACAAGCTGTAATTGAGAATGTTGGGGGGAAAATTTTTACGTTCGGCTCTTACCGACTAGGAGT
ACACACGAAAGGTGCAGATATCGATGCGTTGTGCGTTGCACCAAGACACGTGGATCGAAATGACTTTTTCACCTCCTTCT
ATGACAAATTGAAACTACAGGAGGAAGTAAAAGATTTAAGAGCGGTTGAGGAGGCCTTTGTGCCGGTTATCAAACTGTGT
TTTGATGGAATAGAGATTGATATTTTGTTTGCAAGATTAGCATTGCAGACTATTCCGGAAGATTTGGACCTACGAGATGA
TAGTCTGCTTAAAAATTTAGATATTAGGTGCATAAGAAGCCTTAATGGTTGCCGGGTAACTGATGAAATTTTACACCTAG
TACCAAACATTGACAGCTTCAGGTTAACACTGAGAGCCATCAAATTATGGGCCAAATGCCACAACATCTATTCCAATATA
TTGGGTTTCCTTGGAGGTGTTTCCTGGGCTATGCTGGTAGCAAGAACTTGCCAGCTTTATCCAAATGCAATAGCATCCAC
TCTTGTACGAAAATTTTTCTTGGTATTTTCTGAGTGGGAATGGCCAAATCCAGTCTTGTTAAAAGAACCAGAAGAACGAA
ATCTTAACTTGCCTGTATGGGACCCAAGAGTGAATCCTAGTGACAGGTACCATCTTATGCCTATAATTACACCAGCATAC
CCACAGCAGAACTCCACATACAATGTGTCTGTGTCAACCAGGATGGTCATGATTGAGGAGTTTAAGCAAGGGCTTGCTAT
CACACATGAAATTCTGCTGAATAAGGCAGAATGGTCCAAACTTTTTGAAGCTCCAAGCTTTTTTCAGAAATATAAGCATT
ATATTGTACTACTGGCAAGTGCACCAACAGAGAAACAACATTTAGAGTGGGTGGGCTTGGTGGAATCAAAGATCCGAATC
CTGGTTGGGAGCCTGGAAAAGAATGAATTCATTACTCTGGCACATGTGAATCCCCAGTCATTTCCAGCACCTAAAGAAAA
TGTTGACAAAGAAGAATTTCGTACTATGTGGGTGATTGGGTTAGTGTTGAAAAAGCCAGAAAATTCTGAAATTCTCAGTA
TTGATCTCACTTATGATATTCAGTCTTTCACAGATACAGTGTACAGACAAGCAATAAATAGTAAGATGTTTGAGATGGAT
ATGAAGATTGCTGCAATGCATCTAAGAAGAAAGGAACTTCATCAGCTACTTCCAAATCATGTTCTTCAGAAAAAGGAAAC
ACATTTAACA

Alignment

ORF - retro_rnor_863 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.37 %
• Parental protein coverage: 69.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPFPVTTQGSQQTQPPQRHYGITSPISLAAPKETDCLLTQKLIETLKPFGVFEEEEELQRRILILGKLNN
          MPF.VTTQG.QQ..P....YGI.SPISLAAPK.TD..LTQKLIETL.PFGVFEEEEELQRRILIL.KLNN
Retrocopy MPFAVTTQGAQQPAPAPKQYGISSPISLAAPKDTDRELTQKLIETLQPFGVFEEEEELQRRILILQKLNN

Parental  LVKEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQ
          LVKEWIREISES.NLPQ.VIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDR.DFFTSFYDKLKLQ
Retrocopy LVKEWIREISESRNLPQAVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRNDFFTSFYDKLKLQ

Parental  EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
          EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI
Retrocopy EEVKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEI

Parental  LHLVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWE
          LHLVPNID.FRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLV.KFFLVFS.WE
Retrocopy LHLVPNIDSFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVRKFFLVFSEWE

Parental  WPNPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDE
          WPNPVLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVM.EEFKQGLAIT.E
Retrocopy WPNPVLLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMIEEFKQGLAITHE

Parental  ILLSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
          ILL.KAEWSKLFEAP.FFQKYKHYIVLLASAPTEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQS
Retrocopy ILLNKAEWSKLFEAPSFFQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQS

Parental  FPAPKESPDREEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFELDMKIAAMHVKR
          FPAPKE..D.EEFRTMWVIGLV.KK.ENSE.LS.DLTYDIQSFTDTVYRQAINSKMFE.DMKIAAMH..R
Retrocopy FPAPKENVDKEEFRTMWVIGLVLKKPENSEILSIDLTYDIQSFTDTVYRQAINSKMFEMDMKIAAMHLRR

Parental  KQLHQLLPSHVLQKRKKHST
          K.LHQLLP.HVLQK...H.T
Retrocopy KELHQLLPNHVLQKKETHLT

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	0.29 RPM	79.23 RPM
SRP017611_kidney	0.07 RPM	142.29 RPM
SRP017611_liver	0.00 RPM	81.69 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_rnor_863 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CV113386	16140850	16141547	99.3	675	3	657

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_863 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_863 has 9 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_30
Pan troglodytes	retro_ptro_2595
Gorilla gorilla	retro_ggor_202
Pongo abelii	retro_pabe_3113
Macaca mulatta	retro_mmul_1675
Callithrix jacchus	retro_cjac_1763
Mus musculus	retro_mmus_37
Bos taurus	retro_btau_1078
Canis familiaris	retro_cfam_1783

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000090060	1 retrocopy	retro_hsap_30,
Gorilla gorilla	ENSGGOG00000006287	1 retrocopy	retro_ggor_202,
Loxodonta africana	ENSLAFG00000000946	1 retrocopy	retro_lafr_895,
Myotis lucifugus	ENSMLUG00000010922	1 retrocopy	retro_mluc_1396,
Monodelphis domestica	ENSMODG00000012887	2 retrocopies	retro_mdom_1714, retro_mdom_1916,
Mus musculus	ENSMUSG00000021111	1 retrocopy	retro_mmus_37,
Otolemur garnettii	ENSOGAG00000004611	1 retrocopy	retro_ogar_987,
Procavia capensis	ENSPCAG00000004199	1 retrocopy	retro_pcap_91,
Rattus norvegicus	ENSRNOG00000004827	1 retrocopy	retro_rnor_863 ,