RetrogeneDB ID: retro_rnor_1087

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 15:10370275..10370520(+)
• Located in intron of: ENSRNOG00000014661

Retrocopy information

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

Parental gene information

• Parental gene symbol: Snapc5
• Ensembl ID: ENSRNOG00000010156
• Aliases: None
• Description: snRNA-activating protein complex subunit 5 [Source:RefSeq peptide;Acc:NP_001103113]

Sequence

>retro_rnor_1087
AAAGATGTCCTGTATGACCAACTGGACCACCTTAAAGTTGAAGGATAGGCCCTCCAATCAATGATAAGTTCTCAAAAAGG
GACCGAGACACTGTCTTCTCAGCTTGCACCTGAATAGTTACATGATATGTCACTGAATATAGACAATGAAGCTTCAATCA
ATCAAGGCACACTAAGCTCAGCACAAGGAGCCCTGTGGAAGTGAAGGAAGAAGAGGGGGTGGTGGAGTAGGAAGAATCTG
TTTCA

Alignment

ORF - retro_rnor_1087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.27 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAALHDQLNRLKVEELALQSMINSRGRTETLPSQPAPEQLCDMSLQVDNEASINQTAL-KLSTRSPMEEE
          K..L.DQL..LKVE..ALQSMI.S...TETL.SQ.APE.L.DMSL..DNEASINQ..L.KLSTRSP.E..
Retrocopy KDVLYDQLDHLKVEG*ALQSMISSQKGTETLSSQLAPE*LHDMSLNIDNEASINQGTL<KLSTRSPVEVK

Parental  EEEEEEE-EESDS
          EEE...E.EES.S
Retrocopy EEEGVVE*EESVS

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	24.23 RPM
SRP017611_kidney	0.00 RPM	14.72 RPM
SRP017611_liver	0.00 RPM	6.66 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1087 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1087 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1087 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_702

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017304	1 retrocopy	retro_cfam_1063,
Callithrix jacchus	ENSCJAG00000007484	1 retrocopy	retro_cjac_2314,
Dasypus novemcinctus	ENSDNOG00000006689	1 retrocopy	retro_dnov_1203,
Gorilla gorilla	ENSGGOG00000003693	1 retrocopy	retro_ggor_2398,
Macropus eugenii	ENSMEUG00000003990	1 retrocopy	retro_meug_1590,
Macaca mulatta	ENSMMUG00000016841	1 retrocopy	retro_mmul_1815,
Mus musculus	ENSMUSG00000032398	1 retrocopy	retro_mmus_702,
Nomascus leucogenys	ENSNLEG00000012935	1 retrocopy	retro_nleu_2325,
Oryctolagus cuniculus	ENSOCUG00000008791	1 retrocopy	retro_ocun_1059,
Rattus norvegicus	ENSRNOG00000010156	1 retrocopy	retro_rnor_1087 ,
Ictidomys tridecemlineatus	ENSSTOG00000009201	1 retrocopy	retro_itri_1582,
Tupaia belangeri	ENSTBEG00000014333	1 retrocopy	retro_tbel_68,