RetrogeneDB ID: retro_rnor_520

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:205840122..205840438(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSRNOG00000032769
• Aliases: None
• Description: None

Sequence

>retro_rnor_520
TTTGACCCCTTTGTTGATGCAAGTAAGGGTGATGACCTGCTTCCTGCTGGCACTGAGGATTATATCCATAAAAGAATTCA
ACGGAGAAATGGCAGGAAGACCCTTACCACTCCCTGTCCAGGGGATCACTGATGATTACGATAAAAAGAAACTAGTGAAG
GCATTTAAGAAGAAATCTGCCTGCAACGGTACTGTAATTGAGCATCCAGAATATGGAAAAGTATTTCAGCTACAGGGTGA
CCAGCACAAGAACATATGCCAGTTCCTGACAGAGACTGGACAGGCTAAGGAGGATCAGATGAAGGTTCATGGGTTT

Alignment

ORF - retro_rnor_520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.09 %
• Parental protein coverage: 91.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FDPFDDASKGDDLLPAGTEDDFHIRIQQRN-KKTL-IPVQG-VTDDYNEKKLAKGSLKKFACNGTVIKHA
          FDPF.DASKGDDLLPAGTED..H.RIQ.RN..KTL..P..G..TDDY..KKL.K...KK.ACNGTVI.H.
Retrocopy FDPFVDASKGDDLLPAGTEDYIHKRIQRRNGRKTLTTPCPG>ITDDYDKKKLVKAFKKKSACNGTVIEHP

Parental  EYREIIKLRDDQSNNICQFLIEIGLAKDDQLKNHGF
          EY.....L..DQ..NICQFL.E.G.AK.DQ.K.HGF
Retrocopy EYGKVFQLQGDQHKNICQFLTETGQAKEDQMKVHGF

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	0.22 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_520 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_520 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 59 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008378	7 retrocopies	retro_chof_1435, retro_chof_170, retro_chof_2236, retro_chof_2293, retro_chof_2625, retro_chof_320, retro_chof_708,
Dipodomys ordii	ENSDORG00000013853	4 retrocopies	retro_dord_349, retro_dord_350, retro_dord_663, retro_dord_753,
Equus caballus	ENSECAG00000012516	1 retrocopy	retro_ecab_436,
Loxodonta africana	ENSLAFG00000002852	2 retrocopies	retro_lafr_386, retro_lafr_877,
Mus musculus	ENSMUSG00000035530	27 retrocopies	retro_mmus_1033, retro_mmus_1063, retro_mmus_1191, retro_mmus_1213, retro_mmus_1286, retro_mmus_1392, retro_mmus_1448, retro_mmus_1652, retro_mmus_2045, retro_mmus_2270, retro_mmus_2604, retro_mmus_2737, retro_mmus_2990, retro_mmus_3043, retro_mmus_3047, retro_mmus_308, retro_mmus_3141, retro_mmus_3164, retro_mmus_3386, retro_mmus_3468, retro_mmus_3471, retro_mmus_3638, retro_mmus_3639, retro_mmus_3963, retro_mmus_512, retro_mmus_585, retro_mmus_840,
Rattus norvegicus	ENSRNOG00000032769	1 retrocopy	retro_rnor_520 ,
Rattus norvegicus	ENSRNOG00000033765	15 retrocopies	retro_rnor_1088, retro_rnor_1347, retro_rnor_1518, retro_rnor_1744, retro_rnor_1971, retro_rnor_2067, retro_rnor_2171, retro_rnor_2203, retro_rnor_2532, retro_rnor_2548, retro_rnor_2579, retro_rnor_45, retro_rnor_532, retro_rnor_571, retro_rnor_65,
Sorex araneus	ENSSARG00000006287	1 retrocopy	retro_sara_36,
Sarcophilus harrisii	ENSSHAG00000005729	1 retrocopy	retro_shar_42,