RetrogeneDB ID: retro_rnor_1399

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:51378028..51378375(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Mrpl35
• Ensembl ID: ENSRNOG00000008546
• Aliases: None
• Description: 39S ribosomal protein L35, mitochondrial [Source:RefSeq peptide;Acc:NP_001100066]

Sequence

>retro_rnor_1399
CACCTGGCATCTGGGCATAGTGCAACAGTCCCTGATAGAGTGACCACCTTGGTTCCCAGTGTCCTGAAGCCACCAGTCAG
AACTCTAACATCCTTCAACACATGGAAGGCAAGAGAAAGACAGAAGAGTGGTCTGCTACGCTTCCTTTGATTCCATCTGG
CTTTTGGCTAAGGAGAAAGACTGGTTATAGGAAAAAAATCATGGAAAAAGTCAACTGCAAGAAAGAAGCTCTTGAGGGAA
TTTGTAGAGTCTGCAAGAAGACCCAGAGTAAACTCCGAGAGAAAATGATGATATGTTTCCGGAATAGGTACAACCAGTGG
GCTTAGGATCCTTACCAGATGTACCAT

Alignment

ORF - retro_rnor_1399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.39 %
• Parental protein coverage: 61.7 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HLAYGHTASVLNRVATLVPSVLKPPVRALTYCSARKGKRKTVKSVVHRFLRLH-SGLWLRRKAGYKKKLW
          HLA.GH.A.V..RV.TLVPSVLKPPVR.LT.....K......KS...RFL..H.SG.WLRRK.GY.KK..
Retrocopy HLASGHSATVPDRVTTLVPSVLKPPVRTLTSFNTWKARERQ-KSGLLRFL*FH<SGFWLRRKTGYRKKIM

Parental  KKSTARKKRLREFV-FCNKTQSKLLDKMTTSFWKRRNWYTGDPYQMYH
          .K....K..L......C.KTQSKL..KM...F..R.N....DPYQMYH
Retrocopy EKVNCKKEALEGICRVCKKTQSKLREKMMICFRNRYNQWA*DPYQMYH

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	19.20 RPM
SRP017611_kidney	0.00 RPM	23.24 RPM
SRP017611_liver	0.00 RPM	12.24 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1399 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1399 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_1777

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019467	1 retrocopy	retro_cjac_203,
Dasypus novemcinctus	ENSDNOG00000008329	1 retrocopy	retro_dnov_404,
Homo sapiens	ENSG00000132313	4 retrocopies	retro_hsap_3424, retro_hsap_4784, retro_hsap_595, retro_hsap_681,
Gorilla gorilla	ENSGGOG00000026769	3 retrocopies	retro_ggor_2315, retro_ggor_2979, retro_ggor_526,
Macropus eugenii	ENSMEUG00000004773	1 retrocopy	retro_meug_1703,
Mus musculus	ENSMUSG00000052962	1 retrocopy	retro_mmus_1777,
Nomascus leucogenys	ENSNLEG00000002756	4 retrocopies	retro_nleu_1103, retro_nleu_1362, retro_nleu_2217, retro_nleu_781,
Otolemur garnettii	ENSOGAG00000004048	1 retrocopy	retro_ogar_2600,
Pongo abelii	ENSPPYG00000012214	5 retrocopies	retro_pabe_1817, retro_pabe_2837, retro_pabe_3724, retro_pabe_541, retro_pabe_595,
Pan troglodytes	ENSPTRG00000012152	4 retrocopies	retro_ptro_2325, retro_ptro_3185, retro_ptro_438, retro_ptro_489,
Rattus norvegicus	ENSRNOG00000008546	1 retrocopy	retro_rnor_1399 ,
Tupaia belangeri	ENSTBEG00000015366	10 retrocopies	retro_tbel_1143, retro_tbel_146, retro_tbel_2647, retro_tbel_289, retro_tbel_2892, retro_tbel_3789, retro_tbel_3828, retro_tbel_428, retro_tbel_4379, retro_tbel_627,
Tarsius syrichta	ENSTSYG00000007713	2 retrocopies	retro_tsyr_1128, retro_tsyr_264,