RetrogeneDB ID: retro_rnor_1835

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:151686187..151687063(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ankrd40
• Ensembl ID: ENSRNOG00000002935
• Aliases: None
• Description: ankyrin repeat domain-containing protein 40 [Source:RefSeq peptide;Acc:NP_001128171]

Sequence

>retro_rnor_1835
GAGATTCTTACAACAAAAGGAGAAATGCCAGTACAATTCACATCAAGTAGAGAAATCAGGAAGATTGTGGGAGTAGAAGA
TGATGATGAGGACGAGATCCCCAAGCTGAAGGAGTCAGAACTGCCCTTTGATCTTAACTATCTGACCAACCCAGCCTTCC
CTCTTATCTACACCCCTGCAGCAGAGACTCCACCCAGCTGTAGAGTGGAGGTCCCTCTCCACCTCCAGTGCCCGACCCCT
GCAGATGGCTCACCTCACCTCCATTGCCTCCCCCACAGAACCCCTCTGCCAGGGGCCTTTCCTAGGGAGTCACACCTCTT
TGGCACTGGTCCAGAATGTTGCTATCTCTGGCCCCTCTGCCATACTTAGAACACCAGAAAGATCAAAACCTGGTATTGTC
TGTCAGCCACCAGTGGGGCAGAAATGTTCACTGTTCTCTGTCCCATCCAACCCACCGGTGTCTCTAGAACCTCAAAATGC
TGTACCATATGCAGGACCAGTGCCAGCATCCCAGCCACGTTTCTTCACCGGAGCACTTCCATTAAATATGCAAGAGCTGG
TTCTCAAGGTGAGGTACAGAACCCATCTCTTCATGAAAATGAGTTCATTGAAAGTGAACTTGATCGATAGAAACTCACTT
ACCTAGAATTGTTCAGAGTGAGTTGCTGTGAGCTGAGTGTTAATCCAGACCAAGTGGAAAAGATGATACAGTTACCCAAT
ACTCTGTTAAGAAAGAACAAAGATGTTGCATGAATCCAGGACTTCCAGGAGCTGAAACTGGCTCTGATGATAAGTGAGAA
TAATTTTCTGTTTAGAAACGCTGCATCCTCCCTGACTGAGAGGCCTTGATACAACCCGAGAGCTTCAAACCTGACA

Alignment

ORF - retro_rnor_1835 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76. %
• Parental protein coverage: 80.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EILTTKGEMPVQLTSRREIRKIMGVEEADDDEEIPQLKKESELPFVPNYLANPAFPFIYTPAAE-DATQL
          EILTTKGEMPVQ.TS.REIRKI.GVE..DD..EIP.LK.ESELPF..NYL.NPAFP.IYTPAAE.D.TQL
Retrocopy EILTTKGEMPVQFTSSREIRKIVGVED-DDEDEIPKLK-ESELPFDLNYLTNPAFPLIYTPAAE<DSTQL

Parental  QNGGPSPPPVSPPAEG--SPPLLPP-TEP-PLLGAFPRD-HTSLALVQNGDISAPSAILRTPESTKPGPV
          ..GGPSPPPV..P.....SPPL.PP.TEP.PL.GAFPR..HTSLALVQN..IS.PSAILRTPE..KPG.V
Retrocopy *SGGPSPPPVPDPCRWLTSPPLPPP<TEP<PLPGAFPRE>HTSLALVQNVAISGPSAILRTPERSKPGIV

Parental  CQPPVSQNRSLFSVPSKPPVSLEPQNGT-YAGPAPAFQPFFFTGAFPFNMQELVLKVR-IQNPSLRENDF
          CQPPV.Q..SLFSVPS.PPVSLEPQN...YAGP.PA.QP.FFTGA.P.NMQELVLKVR..QNPSL.EN.F
Retrocopy CQPPVGQKCSLFSVPSNPPVSLEPQNAVPYAGPVPASQPRFFTGALPLNMQELVLKVR<VQNPSLHENEF

Parental  IEIELDRQELTYQELLRVSCCELGVNPDQVEKIRKLPNTLLRKDKDVARLQDFQELELVLTISENNFLFR
          IE.ELDR..LTY.EL.RVSCCEL.VNPDQVEK...LPNTLLRK.KDVA..QDFQEL.L.L.ISENNFLFR
Retrocopy IESELDR*KLTYLELFRVSCCELSVNPDQVEKMIQLPNTLLRKNKDVA*IQDFQELKLALMISENNFLFR

Parental  NPASSLTERPCFNRRASKLT
          N.ASSLTERP..N.RAS.LT
Retrocopy NAASSLTERP*YNPRASNLT

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	93.68 RPM
SRP017611_kidney	0.00 RPM	56.80 RPM
SRP017611_liver	0.00 RPM	15.20 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1835 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1835 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1835 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000012574	1 retrocopy	retro_ecab_937,
Rattus norvegicus	ENSRNOG00000002935	2 retrocopies	retro_rnor_1835 , retro_rnor_755,
Tursiops truncatus	ENSTTRG00000000221	1 retrocopy	retro_ttru_824,