RetrogeneDB ID: retro_tbel_1963

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_6075:50732..51598(+)
• Located in intron of: ENSTBEG00000017652

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRIX1
• Ensembl ID: ENSTBEG00000011652
• Aliases: None
• Description: BRX1, biogenesis of ribosomes, homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24170]

Sequence

>retro_tbel_1963
AAGCGGAAGAATAAGGAACAAATTCTCATCTTTTCTTCCAGAGGAATAAATTTTAGAACAAGACATTTAATGCAGGGCTT
GAGGATGCTGATGCCTCATTCTAAAGCAGATATTAACATGGATCATAAAGATAAATTATTTGTGATGAATGAGGTCTGTG
AAATGAAAAACTGCAATAAGTACATCTATTTTGAAGCTAAGAACAAACAGAATCTCTACATGTGGCTTTCAAATTCCCCT
CATGGACCATCTGCTAAATTCCTTGTTCAAAATATTCATATCCTTGTTGAACTAAAGCTGACCGGAAACTTTGAAAGGTT
CTTGGCCCCTTTTTGTCTTTTGATCCTGCTTTTGATGAATTACCACATTATGTTTTATTAAAAGAACTCCTAATTCAAAT
CTTTAATGCACCACGGTATTATCCTTGAAGTCAACCATTTGTGGACCGTGTGTTTACTTTCACCATTTTGGAAAATAGGA
TATGGTTTTGGAACTTTCGGATCCTAGATGAAGATGCTGCTCCTGTAGAAATAGGACCTCGTTTTGTCCTAAACTCATAA
CGATTTTCCAGGGAAGTTTTGGAGGACCAACTCTATACGAAAATCCTCACTACCAGTCACCACACATGCACTGGCGTGTT
GTAAGATCCATCTCTGCTGCAAAATACAGGGAAGCAGCAAGTGAAGGATGTGCAGAAGCTAAGAAAGAAAGAGCCAAAGA
CGATTCTTCCACATGAACTTACTGAAGATGTTTTTGCTATACCAGCTGAGGAGAAACCAGTAGAAATGCAGTGGGTAAAA
CCAGAGTCAAAAGTCAATTTGAAAGCAAGAAAGAAAAGGATTTACAAAAAGCATAGAACAATGCAA

Alignment

ORF - retro_tbel_1963 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.06 %
• Parental protein coverage: 96.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KWKNKERILIFSSRGINFRTRHLMQDLRTLMPHSKADTKMDRKDKLFVINEVCEMKNCNKCIYFEAKKKQ
          K.KNKE.ILIFSSRGINFRTRHLMQ.LR.LMPHSKAD..MD.KDKLFV.NEVCEMKNCNK.IYFEAK.KQ
Retrocopy KRKNKEQILIFSSRGINFRTRHLMQGLRMLMPHSKADINMDHKDKLFVMNEVCEMKNCNKYIYFEAKNKQ

Parental  DLYMXXXXXXXXXSAN-PVQSIHTLAELKLTGNCLKGSRP-LLSFDPAFDELPHYALLKELLIQIFSTPR
          .LYM.........SA...VQ.IH.L.ELKLTGN......P..LSFDPAFDELPHY.LLKELLIQIF..PR
Retrocopy NLYMWLSNSPHGPSAKFLVQNIHILVELKLTGNFERFLAP<FLSFDPAFDELPHYVLLKELLIQIFNAPR

Parental  YHPKSQPFVDHVFTFTILDHRIWFRNFQIIEEDAALVEIGPRFVLN-LIKIFQGSFGGPTLYENPHYQSP
          Y.P.SQPFVD.VFTFTIL..RIWF.NF.I..EDAA.VEIGPRFVLN.LI.IFQGSFGGPTLYENPHYQSP
Retrocopy YYP*SQPFVDRVFTFTILENRIWFWNFRILDEDAAPVEIGPRFVLN<LITIFQGSFGGPTLYENPHYQSP

Parental  NMHRRIVRSMTAAKYREKQQVKDVQKLRKKEPK-TILPHDPTEDVFAIPAEEKPVEIQWVKPEPKVDLKA
          .MH.R.VRS..AAKYRE...........K...K.TILPH..TEDVFAIPAEEKPVE.QWVKPE.KV.LKA
Retrocopy HMHWRVVRSISAAKYREAAS-EGCAEAKKERAK>TILPHELTEDVFAIPAEEKPVEMQWVKPESKVNLKA

Parental  RKKRIYKRHRKMQ
          RKKRIYK.HR.MQ
Retrocopy RKKRIYKKHRTMQ

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_1963 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1963 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 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001790	2 retrocopies	retro_chof_1664, retro_chof_1776,
Callithrix jacchus	ENSCJAG00000018506	1 retrocopy	retro_cjac_1389,
Homo sapiens	ENSG00000113460	1 retrocopy	retro_hsap_3954,
Gorilla gorilla	ENSGGOG00000004225	1 retrocopy	retro_ggor_2657,
Loxodonta africana	ENSLAFG00000007249	1 retrocopy	retro_lafr_1116,
Myotis lucifugus	ENSMLUG00000029255	3 retrocopies	retro_mluc_1402, retro_mluc_707, retro_mluc_963,
Macaca mulatta	ENSMMUG00000000442	1 retrocopy	retro_mmul_2289,
Monodelphis domestica	ENSMODG00000020386	1 retrocopy	retro_mdom_1032,
Nomascus leucogenys	ENSNLEG00000014452	1 retrocopy	retro_nleu_533,
Otolemur garnettii	ENSOGAG00000014827	2 retrocopies	retro_ogar_3116, retro_ogar_793,
Pongo abelii	ENSPPYG00000015390	2 retrocopies	retro_pabe_3258, retro_pabe_3379,
Pan troglodytes	ENSPTRG00000016784	1 retrocopy	retro_ptro_2684,
Rattus norvegicus	ENSRNOG00000018021	1 retrocopy	retro_rnor_1140,
Tupaia belangeri	ENSTBEG00000011652	9 retrocopies	retro_tbel_1963 , retro_tbel_1964, retro_tbel_2981, retro_tbel_3002, retro_tbel_3082, retro_tbel_4194, retro_tbel_4229, retro_tbel_4418, retro_tbel_954,