RetrogeneDB ID: retro_rnor_2843

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:107517143..107517438(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000049744
• Aliases: None
• Description: Protein Vma21; Similar to 2610030H06Rik protein (Predicted), isoform CRA_b [Source:UniProtKB/TrEMBL;Acc:D3ZM03]

Sequence

>retro_rnor_2843
GAGCTCCTTGACAAAGCAGCCCCAATCCCGTTGCAGCCTCCAGAGTTTAGAAATGAAACATCTTTATCTTTCTCTTCAAT
CTTGAAGACACTCCTGTTCATTACAGCTTTAAGGAGCAGTCCCTATCTGATTGTATTTTACAACTAAATCCTATATATGT
GAAGGTGCTTCTGGAATGTCCAACAGAGACAGCTATTTTTATGCTGCAATTATTGCTGTTCATGTGGTTCTAGCCCTGTT
GGTCTATGTGGCCTGGAACGAAGGCTCGTGACAGTGGCATGAAGGCAAACAGGAT

Alignment

ORF - retro_rnor_2843 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.61 %
• Parental protein coverage: 99.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ERLDKAALNALQPPEFRNENSLA-ATLKTLLFFTALMIT-VPIGLYFTTKSYIFEGALGMSNRDSYFYAA
          E.LDKAA...LQPPEFRNE.SL........L.F.......VPI.LYFTTKSYI.EGA.GMSNRDSYFYAA
Retrocopy ELLDKAAPIPLQPPEFRNETSLSFSSILKTLLFITALRS>VPI*LYFTTKSYICEGASGMSNRDSYFYAA

Parental  IVAVVAVHVVLALFVYVAWNEGSRQWREGKQD
          I.AV...HVVLAL.VYVAWNEGS.QW.EGKQD
Retrocopy IIAV---HVVLALLVYVAWNEGS*QWHEGKQD

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2843 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2843 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2843 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006296	1 retrocopy	retro_btau_1106,
Callithrix jacchus	ENSCJAG00000003916	1 retrocopy	retro_cjac_150,
Dasypus novemcinctus	ENSDNOG00000008426	1 retrocopy	retro_dnov_504,
Echinops telfairi	ENSETEG00000006467	1 retrocopy	retro_etel_528,
Homo sapiens	ENSG00000160131	1 retrocopy	retro_hsap_3724,
Macaca mulatta	ENSMMUG00000009034	1 retrocopy	retro_mmul_1693,
Mus musculus	ENSMUSG00000073131	2 retrocopies	retro_mmus_116, retro_mmus_3675,
Nomascus leucogenys	ENSNLEG00000013711	1 retrocopy	retro_nleu_1971,
Oryctolagus cuniculus	ENSOCUG00000015201	1 retrocopy	retro_ocun_443,
Pongo abelii	ENSPPYG00000020820	1 retrocopy	retro_pabe_3133,
Pan troglodytes	ENSPTRG00000022372	1 retrocopy	retro_ptro_2521,
Rattus norvegicus	ENSRNOG00000049744	1 retrocopy	retro_rnor_2843 ,
Ictidomys tridecemlineatus	ENSSTOG00000011179	1 retrocopy	retro_itri_500,