RetrogeneDB ID: retro_rnor_1600

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:5650191..5650533(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Nme1
• Ensembl ID: ENSRNOG00000002693
• Aliases: None
• Description: Nucleoside diphosphate kinase A [Source:UniProtKB/Swiss-Prot;Acc:Q05982]

Sequence

>retro_rnor_1600
AGGTCGATCATGAGAGAAATCATCCAGCATTTTAAACAGAAGGAATTCCTGCTTGCTGGGTTGAAATTCTTGCAGGTTTC
ACGAGACCTTCTTGAGCATTACATCAACATGAAGGATTGTCTCTTCTTTATTGTTCTGGTAGAGTATAAGCATTCAGGAC
CAGTGGCATCTATGGTCTGGTAGGAGCTGAATGTTGTGAAGACAAGCTGGGTGATGCTTGGAGAGATCAACTCCACAAAC
TCTCAGCCTGGGACCACCCAAAAAGACTTTTACATCCAAGTTGGCAGTAACATCATTCATAGCAGTGGTTCTGTGGAGAG
TGCAGAGAAGGAGATCAGCTTG

Alignment

ORF - retro_rnor_1600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 75.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGLVGEIIKRFEQKGFRLVGLKFIQASEDLLKEHYIDLKDRPFFSGLVKYMHSGPVVAMVWEGLNVVKTG
          R....EII..F.QK.F.L.GLKF.Q.S.DLL.EHYI..KD..FF..LV.Y.HSGPV..MVW..LNVVKT.
Retrocopy RSIMREIIQHFKQKEFLLAGLKFLQVSRDLL-EHYINMKDCLFFIVLVEYKHSGPVASMVW*ELNVVKTS

Parental  RVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEKEISL
          .VMLGE.N...S.PGT...DF.IQVG.NIIH.S.SVESAEKEISL
Retrocopy WVMLGEINSTNSQPGTTQKDFYIQVGSNIIHSSGSVESAEKEISL

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	0.65 RPM	67.37 RPM
SRP017611_kidney	0.21 RPM	25.19 RPM
SRP017611_liver	0.27 RPM	18.36 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1600 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1600 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1600 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004651	1 retrocopy	retro_btau_1707,
Canis familiaris	ENSCAFG00000023628	7 retrocopies	retro_cfam_117, retro_cfam_1645, retro_cfam_37, retro_cfam_676, retro_cfam_69, retro_cfam_832, retro_cfam_96,
Gorilla gorilla	ENSGGOG00000016526	1 retrocopy	retro_ggor_71,
Monodelphis domestica	ENSMODG00000028492	1 retrocopy	retro_mdom_503,
Mustela putorius furo	ENSMPUG00000015559	5 retrocopies	retro_mputfur_1093, retro_mputfur_1357, retro_mputfur_442, retro_mputfur_667, retro_mputfur_997,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081, retro_mmus_581,
Nomascus leucogenys	ENSNLEG00000007919	2 retrocopies	retro_nleu_1029, retro_nleu_1030,
Oryctolagus cuniculus	ENSOCUG00000022135	1 retrocopy	retro_ocun_1728,
Pan troglodytes	ENSPTRG00000009415	1 retrocopy	retro_ptro_91,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Rattus norvegicus	ENSRNOG00000002693	3 retrocopies	retro_rnor_1198, retro_rnor_1600 , retro_rnor_704,
Rattus norvegicus	ENSRNOG00000049152	1 retrocopy	retro_rnor_2679,