RetrogeneDB ID: retro_tbel_994

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_3532:412449..412823(+)
• Located in intron of: ENSTBEG00000013143

Retrocopy information

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

Parental gene information

• Parental gene symbol: MNF1
• Ensembl ID: ENSTBEG00000001380
• Aliases: None
• Description: mitochondrial nucleoid factor 1 [Source:HGNC Symbol;Acc:21237]

Sequence

>retro_tbel_994
ATGGCGGCCAACCGCTACCAGCAGTTGGCTTGTGAGAAATGGCCCGTGAATGAAACCAAACGAGGACAGAACTTGGGCAC
TTGCCTGCAGCAGTGGGTAGCACAGGCCTTTTGGGAGGGAGAAAACACCCAGATTGCAGAGCCCAAGGCCTGTGATCAGA
TGTACCAGACCTTAGTACAACTCCATTCAAACTACTCAAACACAAGTACACTCGCCCCAGAGACACCAGCTTCAGTGGCC
TGTCCATGGAAGAGTACAAGCTGATCCTGTCCACAGATACCCTGGAAAAGTTTAAGAAAATGAATAAAGTCATGCAGAAG
AAACTGCAGGAGAAGTTTGCCCCCAAGGGTCCTGAAGAGAGGCATAAAGCCTGG

Alignment

ORF - retro_tbel_994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.22 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLASRYRRFVKFCEEWPVDETKWGRDLGTYLRQRVAQAFREGENTQIAEPEACDQMYQSLARLHSNY-YK
          M.A.RY......CE.WPV.ETK.G..LGT.L.Q.VAQAF.EGENTQIAEP.ACDQMYQ.L..LHSNY..K
Retrocopy MAANRYQQLA--CEKWPVNETKRGQNLGTCLQQWVAQAFWEGENTQIAEPKACDQMYQTLVQLHSNY<LK

Parental  HKYPRPRDTSFSGLSVEEYKLILSTDTLGEFKEINKGMWKKLQEKFASKGPEEKHKAW
          HKY.RPRDTSFSGLS.EEYKLILSTDTL..FK..NK.M.KKLQEKFA.KGPEE.HKAW
Retrocopy HKYTRPRDTSFSGLSMEEYKLILSTDTLEKFKKMNKVMQKKLQEKFAPKGPEERHKAW

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_994 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_994 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 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031270	1 retrocopy	retro_cfam_1168,
Dasypus novemcinctus	ENSDNOG00000002019	1 retrocopy	retro_dnov_674,
Echinops telfairi	ENSETEG00000006979	2 retrocopies	retro_etel_1912, retro_etel_2009,
Macropus eugenii	ENSMEUG00000005278	3 retrocopies	retro_meug_1335, retro_meug_2027, retro_meug_337,
Monodelphis domestica	ENSMODG00000013996	1 retrocopy	retro_mdom_515,
Mustela putorius furo	ENSMPUG00000003032	1 retrocopy	retro_mputfur_511,
Mus musculus	ENSMUSG00000024208	2 retrocopies	retro_mmus_2543, retro_mmus_3376,
Otolemur garnettii	ENSOGAG00000015604	2 retrocopies	retro_ogar_2127, retro_ogar_2204,
Tupaia belangeri	ENSTBEG00000001380	6 retrocopies	retro_tbel_1486, retro_tbel_1573, retro_tbel_1754, retro_tbel_3269, retro_tbel_361, retro_tbel_994 ,