RetrogeneDB ID: retro_tbel_3988

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_49090:114..823(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRC2
• Ensembl ID: ENSTBEG00000010785
• Aliases: None
• Description: ubiquinol-cytochrome c reductase core protein II [Source:HGNC Symbol;Acc:12586]

Sequence

>retro_tbel_3988
CCCCAAATGAAAGCCACAGCTGAGCCTACTGGAGCTCTTTCACATCCTCAGGACCTTGAGTTTACCAAATTACCTAATGG
CTTTAGTGATTGCTTCTCTGGAAAACTATGCTCCTGCATCAAGAATTGGGTTGTTAATTAAAGCAGGCAGTAGATATGAG
GACTCCAACAACTTGGGAACCTCTCATTTGCTCCGTCTTGCATCCAATTTGACCAAAAAAGGAACATAATCTTTCATGAT
AACCTGTGGAATTGAAGCAGTTGGTGGTAATTTAAGTGTGACTGCGACATGGGAAAACATGGCTTAAACCGTGGAATGCC
TGCAGGATGATGTTGATATTCTGATGGAGTTCCTGCTCAATGTCACCACAGCACCAGAATTTTGTTGATGGGAAGTGGCT
GCTCTTCAGTCTCAGTTAAGGGTTCACAAAGCTGTGGCTTTTCACAATCCACAGGCCTGTGTCATTGAAAATCTACATGC
TGCTGCTTACCAAAATGCTTTGGCTAATTCCCTGTATTGTCCTGACTATAGGATTGGAAAAGTGACATCAGAAGAGTTAC
ACTACTATGTTCAGAACCATTTTACAAGTGCAAAAATGGCTTTGATTTGACTTGGCATGAGTCATCCTGTTCTAAAGCAA
GTTGCTGAACAGTTTCTGAACATGAGGGGTGGGCTTGGTTTGTCTGGTGCAAAGGCCAAATACCGAGGA

Alignment

ORF - retro_tbel_3988 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.3 %
• Parental protein coverage: 52.1 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PKAKATAAPTGALPHPQDLEFTKLPNG-LVIASLENYAPASRIGLFIKAGSRYEDSNNLGTSHLLRLASN
          P..KATA.PTGAL.HPQDLEFTKLPNG.LVIASLENYAPASRIGL.IKAGSRYEDSNNLGTSHLLRLASN
Retrocopy PQMKATAEPTGALSHPQDLEFTKLPNG>LVIASLENYAPASRIGLLIKAGSRYEDSNNLGTSHLLRLASN

Parental  LTTKGASSFKITRGIEAVGGNLSVTATRENMAYTVECLRDDVDILMEFLLNVTTAPEFRRWEVAALQSQL
          LT.KG..SF.IT.GIEAVGGNLSVTAT.ENMA.TVECL.DDVDILMEFLLNVTTAPEF..WEVAALQSQL
Retrocopy LTKKGT*SFMITCGIEAVGGNLSVTATWENMA*TVECLQDDVDILMEFLLNVTTAPEFC*WEVAALQSQL

Parental  RVDKAVAFQNPQARVIENLHAAAYRNALANSLYCPDYRIGKVTSEELHYYVQNHFTSARMALIGLGVSHP
          RV.KAVAF.NPQA.VIENLHAAAY.NALANSLYCPDYRIGKVTSEELHYYVQNHFTSA.MALI.LG.SHP
Retrocopy RVHKAVAFHNPQACVIENLHAAAYQNALANSLYCPDYRIGKVTSEELHYYVQNHFTSAKMALI*LGMSHP

Parental  VLKQVAEQFLNMRGGLGLSGAKAKYRG
          VLKQVAEQFLNMRGGLGLSGAKAKYRG
Retrocopy VLKQVAEQFLNMRGGLGLSGAKAKYRG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_3988 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3988 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021651	2 retrocopies	retro_btau_1008, retro_btau_1668,
Canis familiaris	ENSCAFG00000017756	1 retrocopy	retro_cfam_2075,
Callithrix jacchus	ENSCJAG00000009116	1 retrocopy	retro_cjac_222,
Echinops telfairi	ENSETEG00000001084	1 retrocopy	retro_etel_2087,
Myotis lucifugus	ENSMLUG00000003345	2 retrocopies	retro_mluc_1391, retro_mluc_770,
Monodelphis domestica	ENSMODG00000007645	1 retrocopy	retro_mdom_327,
Mustela putorius furo	ENSMPUG00000016849	1 retrocopy	retro_mputfur_1042,
Oryctolagus cuniculus	ENSOCUG00000003891	2 retrocopies	retro_ocun_604, retro_ocun_739,
Otolemur garnettii	ENSOGAG00000005478	4 retrocopies	retro_ogar_1113, retro_ogar_112, retro_ogar_1934, retro_ogar_82,
Ochotona princeps	ENSOPRG00000000419	1 retrocopy	retro_opri_455,
Sorex araneus	ENSSARG00000010670	1 retrocopy	retro_sara_231,
Tupaia belangeri	ENSTBEG00000010785	1 retrocopy	retro_tbel_3988 ,
Vicugna pacos	ENSVPAG00000010914	1 retrocopy	retro_vpac_640,