RetrogeneDB ID: retro_tbel_2272

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_108266:12950..13501(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED6
• Ensembl ID: ENSTBEG00000002302
• Aliases: None
• Description: mediator complex subunit 6 [Source:HGNC Symbol;Acc:19970]

Sequence

>retro_tbel_2272
CAGATGGTTGGTGTCGAATACATCCCTTTATATGCTCAAGACTCCATTCTTGGTGTCATCTGGAAGCAACAGCAGCAGGC
CCTTGCCCGAGTCATCCCACTAGCTGATTGCTCTGTCATTGCTGGAGAGATCGACCAGGCACCAGGCGTGGGATCAGTTA
TAACTCCAGAGTGCTCACTGCAGCACATGGCATTCAGTCAGCTTTGAGGAAGCTATGTCATCTTGCCCAGTGTCATCCTT
TCCAAAGGGTACTGGTGACACTTGAGAGATCATGGAGAACAAGATAAGGTCAAACCAAAAGCCCAGAGAAAAAAAAAGAA
CTGACTCTATCTTCCAGAGACAGTGTGTGGATGCTCTACTCATAGACCTTAGACAAAACTTTTCACCCAAGTTTGTACAA
GCAAAAGACTGGAGAAAAGCCTGACCCAGTGGGTCAGAGAAAGGAAGAGGCAGAACCTATACCAGAAACTGTGAAATCTG
AAAAGAGCACAAAGAAAGTCCGCCAGACGGTGAGCACGAAAGACCCTCCAGAGAAAAGGATGAGGCGTCAG

Alignment

ORF - retro_tbel_2272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.16 %
• Parental protein coverage: 75.1 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  QMVGVEYILLHAQEPILFIIRKQQRQSPAQVIPLADYYIIAGVIYQAPDLGSVI-NSRVLTAVHGIQSA-
          QMVGVEYI.L.AQ..IL..I.KQQ.Q..A.VIPLAD...IAG.I.QAP..GSVI.NSRVLTA.HGIQSA.
Retrocopy QMVGVEYIPLYAQDSILGVIWKQQQQALARVIPLADCSVIAGEIDQAPGVGSVI<NSRVLTAAHGIQSA<

Parental  FDEAMSYC-RYHP-SKGYWWHFRDHEEQDKAKPKA-KRKEEPSSIFQRQRVDALLVDLRQK-PPKFVQ-Q
          F.EAMS.C...HP.SKGYW.H.RDH.EQDK.KPKA........SIFQRQ.VDALL.DLRQ...PKFVQ.Q
Retrocopy FEEAMSSC>QCHP>SKGYW*HLRDHGEQDKVKPKA>RXXXXTDSIFQRQCVDALLIDLRQNFSPKFVQ>Q

Parental  KTGEKPVPVDQTKKEAEPIPETVKSEEKETTKNVQQTVSTKGPPEKRMRLQ
          KTGEKP.PV.Q.K.EAEPIPETVKSE....TK.V.QTVSTK.PPEKRMR.Q
Retrocopy KTGEKPDPVGQRKEEAEPIPETVKSE--KSTKKVRQTVSTKDPPEKRMRRQ

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_2272 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2272 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000013091	1 retrocopy	retro_fcat_1612,
Myotis lucifugus	ENSMLUG00000017357	1 retrocopy	retro_mluc_265,
Monodelphis domestica	ENSMODG00000007174	3 retrocopies	retro_mdom_1190, retro_mdom_524, retro_mdom_625,
Otolemur garnettii	ENSOGAG00000001311	1 retrocopy	retro_ogar_2597,
Ochotona princeps	ENSOPRG00000008957	1 retrocopy	retro_opri_820,
Sorex araneus	ENSSARG00000002553	1 retrocopy	retro_sara_495,
Tupaia belangeri	ENSTBEG00000002302	1 retrocopy	retro_tbel_2272 ,