RetrogeneDB ID: retro_rnor_1529

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:124316801..124317278(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sdhd
• Ensembl ID: ENSRNOG00000022980
• Aliases: None
• Description: Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q6PCT8]

Sequence

>retro_rnor_1529
ATGGCAGTTCTTTTAAAGCTAGGCATTCTCTGCGGTGGTCAAGGAGCTCGAGCTCTGTTACTCTGAAGCTGGATGGTCAG
AACTGCTCATGTGCCAGCATTTCTCTAGGACCAGCCTACCCCGGGATTGCGTGGTACCCAGCACATTCACCTGTCACCCA
GCCACCATTCTGGTTTCAAGGCTACATCTCTCCACTGGACCAGTAAGAGCGTTGTCGGTGTTTTGTCCTTGGGCCTGCTT
TCAGTTGGGTACTTGAATCCCTGTTCTTTGGTGCACTACTCTCTGGCTGCCGCCCTCACTCTGCACACTCACTGGGGCCT
TGGACAAGTGGTTATTGATTACATTCATGGAGACACACTGCAGAAGGCTGTCAAGAGAGGCCACTTGGCACACTCAGCTT
TGACCTTTGCTGGGCTTTGCTACTTCAATTACCACAATGTAGGCATCTGTAGAGAAGTTGTCATGCTGTGGAAGCTC

Alignment

ORF - retro_rnor_1529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.99 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVLLKLGVLCSGQGARALSLRSRAVRPAFVSAFLQDQPTPGWRGTQHIHLSPSHQSGSKAASLHWTSER
          MAVLLKLG.LC.GQGARAL.L.S..VR.A.V.AFL.DQPTPG.RGTQHIHLSPSH.SG.KA.SLHWTS..
Retrocopy MAVLLKLGILCGGQGARALLL*SWMVRTAHVPAFL*DQPTPGLRGTQHIHLSPSHHSGFKATSLHWTSKS

Parental  VVSVLLLGLIPAGYLNPCSVVDYSLAAALTLHSHWGIGQVVTDYVHGDALQKATKAGLLAVSALTFAGLC
          VV.VL.LGL...GYLNPCS.V.YSLAAALTLH.HWG.GQVV.DY.HGD.LQKA.K.G.LA.SALTFAGLC
Retrocopy VVGVLSLGLLSVGYLNPCSLVHYSLAAALTLHTHWGLGQVVIDYIHGDTLQKAVKRGHLAHSALTFAGLC

Parental  YFNYHDVGICRAVAMLWKL
          YFNYH.VGICR.V.MLWKL
Retrocopy YFNYHNVGICREVVMLWKL

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	57.59 RPM
SRP017611_kidney	0.00 RPM	229.23 RPM
SRP017611_liver	0.00 RPM	80.75 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1529 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1529 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1529 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004066	3 retrocopies	retro_amel_1556, retro_amel_1588, retro_amel_998,
Erinaceus europaeus	ENSEEUG00000013091	1 retrocopy	retro_eeur_336,
Echinops telfairi	ENSETEG00000008424	1 retrocopy	retro_etel_252,
Felis catus	ENSFCAG00000022580	3 retrocopies	retro_fcat_1371, retro_fcat_175, retro_fcat_492,
Homo sapiens	ENSG00000204370	8 retrocopies	retro_hsap_124, retro_hsap_1912, retro_hsap_2132, retro_hsap_2182, retro_hsap_2729, retro_hsap_2784, retro_hsap_355, retro_hsap_3791,
Gorilla gorilla	ENSGGOG00000026496	1 retrocopy	retro_ggor_50,
Loxodonta africana	ENSLAFG00000002763	1 retrocopy	retro_lafr_432,
Myotis lucifugus	ENSMLUG00000012228	3 retrocopies	retro_mluc_2418, retro_mluc_457, retro_mluc_756,
Macaca mulatta	ENSMMUG00000015247	1 retrocopy	retro_mmul_224,
Rattus norvegicus	ENSRNOG00000022980	3 retrocopies	retro_rnor_1529 , retro_rnor_1686, retro_rnor_744,
Sus scrofa	ENSSSCG00000015034	3 retrocopies	retro_sscr_1060, retro_sscr_626, retro_sscr_627,
Tursiops truncatus	ENSTTRG00000010520	5 retrocopies	retro_ttru_1554, retro_ttru_238, retro_ttru_616, retro_ttru_633, retro_ttru_885,