RetrogeneDB ID: retro_rnor_1515

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:106629931..106630388(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Cox11
• Ensembl ID: ENSRNOG00000046318
• Aliases: None
• Description: Protein Cox11; RCG35252 [Source:UniProtKB/TrEMBL;Acc:D3ZNJ0]

Sequence

>retro_rnor_1515
GGACTTAGACAATCACTAGTGGCCAGGCATGCGTCAGACCAGATTGAAAACATGGTGCCTGTTATGGATCAAATCATTAA
GGTAACCTTCAATGCTAACTTTCATACCAGTCTCCAATGGAACCTCAGATCTCAGCAAACAGAAATATATGTGGTACCAG
AAGAGACTGCACTGGCATTTTATAAAGCTAAGAATCCTACTGACAAACCAGTAATTGGGATTTCTACATGTGATGTTGCA
CTGTTTGAAGTCAGACAGTATTTCAACAAAGTACAGTGCTTCTGTTTTGAAGAACAAAGGCTTAGTACACAAGAAGAAGT
AGATATGCCAGTGTTTTTCAACATTGATCCTGAATTTGCAGAAAAATCCAAGAATGGTGAATGTCGATCTCATCACTCTT
TCTTATACTTTTTTTGATGGTAAAGAAGGCCACGAGTTGCCAATTCTAGGCTGTAAT

Alignment

ORF - retro_rnor_1515 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.74 %
• Parental protein coverage: 55.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLGGSAVAGHASDQIENMVPVKDRIIKVTFNADVHASLQWNFRPQQTEIYVVPGETALAFYKAKNPTDKP
          GL..S.VA.HASDQIENMVPV.D.IIKVTFNA..H.SLQWN.R.QQTEIYVVP.ETALAFYKAKNPTDKP
Retrocopy GLRQSLVARHASDQIENMVPVMDQIIKVTFNANFHTSLQWNLRSQQTEIYVVPEETALAFYKAKNPTDKP

Parental  VIGISTYNVVPFEAGQYFNKIQCFCFEEQRLNPQEEVDMPVFFYIDPEFAE-DPRMVNVDLITLSYTFFE
          VIGIST..V..FE..QYFNK.QCFCFEEQRL..QEEVDMPVFF.IDPEFAE..PRMVNVDLITLSYTFF.
Retrocopy VIGISTCDVALFEVRQYFNKVQCFCFEEQRLSTQEEVDMPVFFNIDPEFAE>NPRMVNVDLITLSYTFFD

Parental  AKEGHKLAVPGYN
          .KEGH.L...G.N
Retrocopy GKEGHELPILGCN

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	4.53 RPM
SRP017611_kidney	0.07 RPM	2.79 RPM
SRP017611_liver	0.00 RPM	2.35 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1515 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1515 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1515 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008482	1 retrocopy	retro_cpor_1340,
Dasypus novemcinctus	ENSDNOG00000014862	1 retrocopy	retro_dnov_1933,
Dipodomys ordii	ENSDORG00000001207	1 retrocopy	retro_dord_180,
Homo sapiens	ENSG00000166260	1 retrocopy	retro_hsap_3442,
Microcebus murinus	ENSMICG00000005225	1 retrocopy	retro_mmur_1119,
Monodelphis domestica	ENSMODG00000014855	1 retrocopy	retro_mdom_952,
Mus musculus	ENSMUSG00000020544	4 retrocopies	retro_mmus_1318, retro_mmus_2318, retro_mmus_2714, retro_mmus_986,
Nomascus leucogenys	ENSNLEG00000007990	1 retrocopy	retro_nleu_2297,
Ochotona princeps	ENSOPRG00000004138	1 retrocopy	retro_opri_441,
Pongo abelii	ENSPPYG00000008259	2 retrocopies	retro_pabe_156, retro_pabe_2847,
Pan troglodytes	ENSPTRG00000009422	1 retrocopy	retro_ptro_2335,
Rattus norvegicus	ENSRNOG00000046318	1 retrocopy	retro_rnor_1515 ,