RetrogeneDB ID: retro_tbel_292

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_1669:42967..43285(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000005517
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MED4
• Ensembl ID: ENSTBEG00000014259
• Aliases: None
• Description: mediator complex subunit 4 [Source:HGNC Symbol;Acc:17903]

Sequence

>retro_tbel_292
CAGGTCCTGGAGTTGTTAATTCACCAAGATGGGGAATTTCAAGAACTAATGAACTTGGCCCTTAATCAGGGAAAAATCCA
TCATGAAATACAGGTTTTAGAAAAAGAAGTAGAGAAGAGAGACAGTGATATTCAGCAACTACAAAACCAGCTAAAGGAAG
CAGAACAAATACTGGCAACAGCTGTTTATCAAACAAAAGAGAAACTCAAGTCGATAGAGAAAGCAAGAAAAGGTGCTATC
TCCTCTGAAGAAATAATTAAGTACGCACACAGGATAAGTGCACATAATGCTGTATGTGCCCGACTGACCTGCGTTCCA

Alignment

ORF - retro_tbel_292 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.45 %
• Parental protein coverage: 62.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVLELLIHRDGEFQELMKLALNQGKIHHEMQVLEKEVEKRDSDIQQLQKQLKEAEQILATAVYQAKEKLK
          QVLELLIH.DGEFQELM.LALNQGKIHHE.QVLEKEVEKRDSDIQQLQ.QLKEAEQILATAVYQ.KEKLK
Retrocopy QVLELLIHQDGEFQELMNLALNQGKIHHEIQVLEKEVEKRDSDIQQLQNQLKEAEQILATAVYQTKEKLK

Parental  SIEKARKGAISSEEIIKYAHRISASNAVCAPLTWVP
          SIEKARKGAISSEEIIKYAHRISA.NAVCA.LT.VP
Retrocopy SIEKARKGAISSEEIIKYAHRISAHNAVCARLTCVP

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_292 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_292 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003718	1 retrocopy	retro_amel_1882,
Canis familiaris	ENSCAFG00000004451	1 retrocopy	retro_cfam_1792,
Callithrix jacchus	ENSCJAG00000009256	1 retrocopy	retro_cjac_3937,
Dasypus novemcinctus	ENSDNOG00000018064	1 retrocopy	retro_dnov_1342,
Myotis lucifugus	ENSMLUG00000009265	1 retrocopy	retro_mluc_178,
Mustela putorius furo	ENSMPUG00000001437	1 retrocopy	retro_mputfur_162,
Mus musculus	ENSMUSG00000022109	1 retrocopy	retro_mmus_3576,
Sorex araneus	ENSSARG00000001473	1 retrocopy	retro_sara_353,
Tupaia belangeri	ENSTBEG00000014259	1 retrocopy	retro_tbel_292 ,