RetrogeneDB ID: retro_tbel_1541

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5038:452697..453271(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000001946
• Aliases: None
• Description: None

Sequence

>retro_tbel_1541
TGCCAAGATTTGAAGTTGACATTTGATATTACCTTCTCACCAAACATGGGAAAGGAAAGAGTAAAATAAAATTCTCTTAC
AAGAGGGAGTGTATAAACCTTAGGTGTGATGTTCATTTTGATTTTGCCGGACCTTCAAACCATGGTTCAGCTTTCTTTGG
CTATGAGGATGGTTTTGCTGGCTGCCACATGACCTTTGACAGTGCCAAATCAAAGCTGATAAGGAATAACTTTGCAGTGG
CCTACAGGACTAGAGACTTCTAGCTACACACTAATGTCCTGATGGGACAGAATTTGGAGGATCAATTTATCAGAAACCAT
GTGAAGATCTTAACCCATCAGTAAACCTTGCTTGGACCTCAGGCACCAACTGTACTCATTTTGGTAATGCAGCTTAATAT
CAGTTGGATCCCATTGCATCCATTTCTACACCAGTCAACAATTCTAGTTCAATTGGAGTGGGCTACACTTAGACTCTGAG
GACTGGTCTGAAGCTTACACTGTGTACTCTGGTGAATGGAAAGAGAATTGATGCTGGAGGCCACAAATTTGACCTTGCCC
TGGAGTTGGAGGCT

Alignment

ORF - retro_tbel_1541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.46 %
• Parental protein coverage: 64.95 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CQGLKLTFAKTFSPNMGKK-SGKMKSSYKRESIDLGCDVDFDFAGLAIHGSAVFGRE-GLGGYPMTFDSA
          CQ.LKLTF..TFSPNMGK....K.K.SYKRE.I.L.CDV.FDFAG...HGSA.FG.E.G..G..MTFDSA
Retrocopy CQDLKLTFDITFSPNMGKE<KSKIKFSYKRECINLRCDVHFDFAGPSNHGSAFFGYEDGFAGCHMTFDSA

Parental  KSKLTTNNFPVGYRTGDFQLHTNV-NDGTEFGGSIYQKVCEDLDTSINLAWLSGTNYTSFGIATKYHLDP
          KSKL..NNF.V.YRT.DF.LHTNV..DGTEFGGSIYQK.CEDL..S.NLAW.SGTN.T.FG.A..Y.LDP
Retrocopy KSKLIRNNFAVAYRTRDF*LHTNV<PDGTEFGGSIYQKPCEDLNPSVNLAWTSGTNCTHFGNAA*YQLDP

Parental  TVSFSVKVNNSSLIGVDYTQT-KPDVKL-MSALVDGKSINAGVYKLGLAMELEA
          ..S.S..VNNSS.IGV.YT.T.....KL....LV.GK.I.AG..K..LA.ELEA
Retrocopy IASISTPVNNSSSIGVGYT*TLRTGLKLTLCTLVNGKRIDAGGHKFDLALELEA

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_1541 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1541 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 25 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012975	2 retrocopies	retro_btau_1252, retro_btau_1389,
Canis familiaris	ENSCAFG00000015398	1 retrocopy	retro_cfam_376,
Callithrix jacchus	ENSCJAG00000001145	1 retrocopy	retro_cjac_2385,
Erinaceus europaeus	ENSEEUG00000008623	2 retrocopies	retro_eeur_192, retro_eeur_343,
Felis catus	ENSFCAG00000026943	3 retrocopies	retro_fcat_1385, retro_fcat_804, retro_fcat_815,
Homo sapiens	ENSG00000165637	1 retrocopy	retro_hsap_2114,
Gorilla gorilla	ENSGGOG00000005861	5 retrocopies	retro_ggor_1677, retro_ggor_1949, retro_ggor_2934, retro_ggor_3036, retro_ggor_425,
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Microcebus murinus	ENSMICG00000017815	1 retrocopy	retro_mmur_191,
Myotis lucifugus	ENSMLUG00000007500	2 retrocopies	retro_mluc_1710, retro_mluc_2252,
Macaca mulatta	ENSMMUG00000008691	1 retrocopy	retro_mmul_2200,
Mustela putorius furo	ENSMPUG00000003268	1 retrocopy	retro_mputfur_354,
Mus musculus	ENSMUSG00000021771	1 retrocopy	retro_mmus_2667,
Nomascus leucogenys	ENSNLEG00000016857	1 retrocopy	retro_nleu_1608,
Otolemur garnettii	ENSOGAG00000030039	1 retrocopy	retro_ogar_2116,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Sorex araneus	ENSSARG00000011194	2 retrocopies	retro_sara_300, retro_sara_59,
Sarcophilus harrisii	ENSSHAG00000012048	1 retrocopy	retro_shar_325,
Sus scrofa	ENSSSCG00000010320	2 retrocopies	retro_sscr_681, retro_sscr_791,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541 , retro_tbel_1885, retro_tbel_4597,
Tupaia belangeri	ENSTBEG00000003852	4 retrocopies	retro_tbel_1282, retro_tbel_2613, retro_tbel_3818, retro_tbel_4546,
Tupaia belangeri	ENSTBEG00000007420	4 retrocopies	retro_tbel_1801, retro_tbel_2150, retro_tbel_2261, retro_tbel_884,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
Tursiops truncatus	ENSTTRG00000000371	3 retrocopies	retro_ttru_116, retro_ttru_1172, retro_ttru_776,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,