RetrogeneDB ID: retro_rnor_2983

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:131108082..131108385(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rangrf
• Ensembl ID: ENSRNOG00000004980
• Aliases: Rangrf, RGD1563195
• Description: ran guanine nucleotide release factor [Source:RefSeq peptide;Acc:NP_001099260]

Sequence

>retro_rnor_2983
GTTCATGTGCTATCTGTGCAGCTTCTCTGCTTGAGAGGCTGCTGTCAAGATGCCTAGTTCCTTTCTGGCAAACAGCAGGT
AGCTAAGGAAAACCAGCAGGTAGCAAAGGATGTCACATGGCAGCAAGCCACGCTTCAGCTGCCCCAGTATCAGACCTATA
GTTTGCTCACCTTCAATGAGCTCCCATGTCACAGCAGGTCTCTCGGCCTTGAAAAGCTGTCATGTCCACCTTGGAGCTAG
GGTAACTTTGAACAGCTGGTAACTAGTTTGACTCCTCATGATTCCAACTTCTTTGGTCCCCAG

Alignment

ORF - retro_rnor_2983 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.23 %
• Parental protein coverage: 54.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VQPLCLENLSLRGCCQDAWFLSGKQQVAKENQQVAKDVTLHQALLRLPQYQTDLLLTFNQPPCHSRPLGP
          V..L....L.LRGCCQDA.FLSGKQQVAKENQQVAKDVT..QA.L.LPQYQT..LLTFN..PCHSR.LG.
Retrocopy VHVLSVQLLCLRGCCQDA*FLSGKQQVAKENQQVAKDVTWQQATLQLPQYQTYSLLTFNELPCHSRSLGL

Parental  ENLSCPPWSLGNFEQLVTSLTLHDPNLFGPQ
          E.LSCPPWS.GNFEQLVTSLT.HD.N.FGPQ
Retrocopy EKLSCPPWS*GNFEQLVTSLTPHDSNFFGPQ

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	7.48 RPM
SRP017611_kidney	0.00 RPM	24.49 RPM
SRP017611_liver	0.00 RPM	3.90 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2983 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2983 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2983 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012555	1 retrocopy	retro_chof_14,
Dasypus novemcinctus	ENSDNOG00000018164	1 retrocopy	retro_dnov_2261,
Dipodomys ordii	ENSDORG00000007147	2 retrocopies	retro_dord_325, retro_dord_346,
Macropus eugenii	ENSMEUG00000006399	2 retrocopies	retro_meug_1091, retro_meug_220,
Mus musculus	ENSMUSG00000032892	2 retrocopies	retro_mmus_175, retro_mmus_2983,
Rattus norvegicus	ENSRNOG00000004980	4 retrocopies	retro_rnor_1148, retro_rnor_2982, retro_rnor_2983 , retro_rnor_759,