RetrogeneDB ID: retro_tbel_454

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_2118:1734..2120(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN6
• Ensembl ID: ENSTBEG00000013280
• Aliases: None
• Description: prefoldin subunit 6 [Source:HGNC Symbol;Acc:4926]

Sequence

>retro_tbel_454
ATGGCTGAGCTGATTCAGAAAAAGCTGTAGGTAGAAGTGGGAAAATAGCAACAGCTACAGAAGACTTTAAAGAAAGCCTT
GTCTGGGAAACAGAAGCTTGAAACACAACTAACAGAAAATAATATTGTGAAGGAGGAATTGACCCTGCTGGATGTGTTCA
ACATGGTCTCTAAACTTTTGGGTCCAGTGCTGGTTAAACAGGAGCTGGGGAGCCTTAGGCCACAGTGGGGAAGTGGCTGA
ACTATACCACAGCTGAAATTCAGTGATAAGAATCCCGGCTCCAGGATCTCAAGCAGCAGTCAGAGCCACAGTGGGGAGAG
CCTTGCTCAGCTGCAGCAGGAGTTCAGAGGGACCAGGCAGCAATGGCAGGCACTTCTAGAAAGGCC

Alignment

ORF - retro_tbel_454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAELIQKKLQGEVEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELG
          MAELIQKKL..EV.K.QQLQK.L.K..SG.QKLE.QLTENNIVKEEL.LLD..N.V.KLLGPVLVKQELG
Retrocopy MAELIQKKL*VEVGK*QQLQKTLKKALSGKQKLETQLTENNIVKEELTLLDVFNMVSKLLGPVLVKQELG

Parental  EAR-ATVGKRLDYITAEIKRYESQLRDLERQSEQQ-RETLAQLQQEF-QRAQAAKAGTSGKA
          ..R.ATVGK.L.Y.TAEI...ES.L.DL..QSE.Q..E.LAQLQQEF.QR.QAA.AGTS.KA
Retrocopy SLR<ATVGKWLNYTTAEIQ**ESRLQDLKQQSEPQ>GESLAQLQQEF<QRDQAAMAGTSRKA

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_454 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_454 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
Ailuropoda melanoleuca	ENSAMEG00000001576	2 retrocopies	retro_amel_221, retro_amel_824,
Bos taurus	ENSBTAG00000010723	1 retrocopy	retro_btau_619,
Cavia porcellus	ENSCPOG00000019520	1 retrocopy	retro_cpor_570,
Dipodomys ordii	ENSDORG00000013828	1 retrocopy	retro_dord_453,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Microcebus murinus	ENSMICG00000000922	1 retrocopy	retro_mmur_1520,
Mus musculus	ENSMUSG00000024309	1 retrocopy	retro_mmus_1930,
Oryctolagus cuniculus	ENSOCUG00000010559	1 retrocopy	retro_ocun_711,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Rattus norvegicus	ENSRNOG00000000473	2 retrocopies	retro_rnor_2216, retro_rnor_2869,
Sorex araneus	ENSSARG00000006330	2 retrocopies	retro_sara_338, retro_sara_453,
Tupaia belangeri	ENSTBEG00000013280	1 retrocopy	retro_tbel_454 ,