RetrogeneDB ID: retro_rnor_2628

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 8:58159889..58161119(-)
• Located in intron of: ENSRNOG00000013610

Retrocopy information

• Ensembl ID: ENSRNOG00000023038
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zc3h15
• Ensembl ID: ENSRNOG00000005256
• Aliases: None
• Description: Zinc finger CCCH domain-containing protein 15 [Source:UniProtKB/Swiss-Prot;Acc:Q6U6G5]

Sequence

>retro_rnor_2628
ATGCCCCCCAAGAAACAGGCTTAGGCTGGGGACAGCAACAAGGCAGAGCAGAAGAAGGAGATCATTGAGGACAAAACTTT
TGGACTAAAGAATAAGAAGGGAGCAAAGCGACAGAAATTTATTAAGGCTGTCGCTCATCAAGTGAAATTTGGACAACAGA
ATCCACATCAGGTAGCACAAAGTGAAGCTGAAAAGAAGTTGGAGAAAGAACCACAAGAACTACATGGGTTGTTCAAACTG
GTTGTTGCTGCACAAAAAATAAGTAAAGGTGGGGACCTCAAATCTGTGGTGTGCGCATTCTTCAGACAGGGACAGTGGAC
TAAAGGAGGTGAGTGTAGGTTCTCTCATGACCCCACTTGGGAGAGAAGATGTGAAAAGCGAAGTGTTTACATTGATGCAA
GAGACGACGAACTTGAAAAGGATACTGTGGATAACTGGGATGAGAAGAGGCTGGAAGAAGTAGAAAACGAGAAGCACAGT
GAGGCGGAAAGAAAAAAACAAAAACTCAAATAGTGTGCATTTTCTTGAAGCTATTGAAAATAACAAGTATGGCTGCTTTG
GGTGTGCCCTGGAGGTGGGGACAATTGCATGTATCGCCTCGCACTTCCTCCTGGGTTTGTGCTAAAGAAAGACAAAAAGA
AAGAAGAGAAAAACGACGAAATCTCACTAGAAGATCTAACTGAAAGAGGGGGTTCTGCCCTAGGTCCAAATGTTACCAAA
ATCACTCTAGAATCTTTTCTCCCATGGAAGAAAAGGAAAGGACAAGAAAAGATTGATAAACTTGAACAAGATATGGAGAG
GCGGAAAGCTGACTGAAAGCAGGGAAGCGCTGGTGATCAGTGGTCATGAGGTATTTGAATTCCGTCCTGAGTTGGTCAAT
GATGACGGCGAGGAAGCAGACAATACCCGTTATATTCAGGGAACAGGAGGTGATGAGGTTGATGACTCTGTGGGTGTAAA
TGACATAGATCTAAGCCTGCACGTCCCAAGAGATGTAGAAGAGACAGGGGTCACTGTGGCCAGTCTTGAAAGATCAGCAC
ATATGCGTCAGATAGAGACGAGAACAAATTGAGTGAAACTTCTGGAGGTCTGGCTGAAAATGGTGAAAGAAGTGATTTGG
ACGAGGTCAGCGGAGGGGGAGGACAGGAAAATGGGTCCATCGATGCTGTTCCTGTTGATGGCGAAGATCTGGATGAACTA
GAAGAAGAATTAGACACACTTGATTCAGAA

Alignment

ORF - retro_rnor_2628 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.87 %
• Parental protein coverage: 98.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MPPKKQAQAGGSKKAEQKKKEKIIEDKTFGLKNKKGAKQQKFIKAVTHQVKFGQQNPRQVAQSEAEKKLK
          MPPKKQA.AG.S.KAEQKK...IIEDKTFGLKNKKGAK.QKFIKAV.HQVKFGQQNP.QVAQSEAEKKL.
Retrocopy MPPKKQA*AGDSNKAEQKKE--IIEDKTFGLKNKKGAKRQKFIKAVAHQVKFGQQNPHQVAQSEAEKKLE

Parental  KDDKKKELQELNELFKPVVAAQKISKGADPKSVVCAFFKQGQCTKGDKCKFSHDLTLERKCEKRSVYIDA
          K.....EL..L..L...VVAAQKISKG.D.KSVVCAFF.QGQ.TKG..C.FSHD.T.ER.CEKRSVYIDA
Retrocopy KE--PQELHGLFKL---VVAAQKISKGGDLKSVVCAFFRQGQWTKGGECRFSHDPTWERRCEKRSVYIDA

Parental  RDEELEKDTMDNWDEKKLEEVVNKKHGEAE-KKKPKTQIVCRHFLE-AIENNKYGWF-WVCPGGGDNCMY
          RD.ELEKDT.DNWDEK.LEEV.N.KH.EAE.K.....QIVC..FL..AIENNKYG.F.WVCPGGGDNCMY
Retrocopy RDDELEKDTVDNWDEKRLEEVENEKHSEAE<KXXXXXQIVC-IFLK<AIENNKYGCF<WVCPGGGDNCMY

Parental  RHALPPGFVLKKDKKKEEKEDEISLEDLIERERSALGPNVTKITLESFLAWKKRKRQEKIDKLEQDMERR
          R.ALPPGFV...........DEISLEDL.ER..SALGPNVTKITLESFL.WKKRK.QEKIDKLEQDMERR
Retrocopy RLALPPGFVXXXXXXXXXXXDEISLEDLTERGGSALGPNVTKITLESFLPWKKRKGQEKIDKLEQDMERR

Parental  KAD-FKAGK-ALVISGREVFEFRPELVNDDDEEADDTRYIQGTGGDEVDDSVGVNDIDLSLYVPRDVEET
          KAD..KAGK.ALVISG.EVFEFRPELVNDD.EEAD.TRYIQGTGGDEVDDSVGVNDIDLSL.VPRDVEET
Retrocopy KAD<LKAGK<ALVISGHEVFEFRPELVNDDGEEADNTRYIQGTGGDEVDDSVGVNDIDLSLHVPRDVEET

Parental  GITVASLER-FSTYASDKDENKLSEASGGLAENGERSDLDEDSGGGGQENGSIDAVPVD-ENLFTGE-DL
          G.TVASLER..STYASD.DENKLSE.SGGLAENGERSDLDE.SGGGGQENGSIDAVPVD.E.L...E..L
Retrocopy GVTVASLER<ISTYASDRDENKLSETSGGLAENGERSDLDEVSGGGGQENGSIDAVPVDGEDLDELEEEL

Parental  DELEEE
          D.L..E
Retrocopy DTLDSE

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	47.16 RPM
SRP017611_kidney	0.00 RPM	46.75 RPM
SRP017611_liver	0.07 RPM	23.94 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2628 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2628 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2628 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021762	1 retrocopy	retro_btau_1223,
Choloepus hoffmanni	ENSCHOG00000011958	1 retrocopy	retro_chof_2120,
Callithrix jacchus	ENSCJAG00000005931	2 retrocopies	retro_cjac_2883, retro_cjac_3986,
Cavia porcellus	ENSCPOG00000012965	2 retrocopies	retro_cpor_1294, retro_cpor_919,
Dipodomys ordii	ENSDORG00000011664	1 retrocopy	retro_dord_666,
Loxodonta africana	ENSLAFG00000001563	1 retrocopy	retro_lafr_941,
Myotis lucifugus	ENSMLUG00000007741	2 retrocopies	retro_mluc_1494, retro_mluc_2467,
Monodelphis domestica	ENSMODG00000027565	5 retrocopies	retro_mdom_1230, retro_mdom_1321, retro_mdom_1744, retro_mdom_1942, retro_mdom_871,
Oryctolagus cuniculus	ENSOCUG00000011903	1 retrocopy	retro_ocun_886,
Otolemur garnettii	ENSOGAG00000002182	2 retrocopies	retro_ogar_1093, retro_ogar_611,
Ochotona princeps	ENSOPRG00000015790	2 retrocopies	retro_opri_169, retro_opri_609,
Pan troglodytes	ENSPTRG00000012717	1 retrocopy	retro_ptro_348,
Rattus norvegicus	ENSRNOG00000005256	4 retrocopies	retro_rnor_2628 , retro_rnor_284, retro_rnor_662, retro_rnor_925,
Sorex araneus	ENSSARG00000012071	1 retrocopy	retro_sara_363,