RetrogeneDB ID: retro_tbel_3062

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_128925:247504..248000(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000012523
• Aliases: None
• Description: None

Sequence

>retro_tbel_3062
AAGTACTTCAACATTGGGAGCCAGGGGTCCTGCCTAAAGTGCCAGGAGTAGTGGCTGCAGGGCAAGGTGGTAGCCTTCAA
CTATCAGTCTACACTGCTGACTTTACAAGGTGCCTCTTCGGGTGGAAAGCCCAACCATGCAGACATCTTGCTCATAAACT
TAGAGCATGTTTCAGATGTGGCAATAATGAATGACCACCCAGAAACCCCAGCTCCCCTAGCTTCACTCAGTGTCAGTAAG
CTTGCCAGCAAAGCCCGGACCAAGAAGGAGAAGCTGAGCCAGGCCTATGAATCAGTTCTGGTGTCTCCCTAGAAGGCCAG
CAGCTCTTCCAGATCATCCGACAAGACCATTAAAGACTGTAAATGGCAAGAAAAAAGCATCATAGTCATGGAAGAAGCTG
TTATCACACCCATATCAAGTATAAATCTGTAAAGGCAAAGAGGGGTGTACACTGAGCCATGTACACAAAACAGTTGAAAA
ACATTTTAGAGATGTA

Alignment

ORF - retro_tbel_3062 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.59 %
• Parental protein coverage: 85.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EYFSVGSQVSCRTCQEQRLQGEVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSEVEIINDRTETP
          .YF..GSQ.SC..CQE..LQG.VVAF.YQS..L.L...SS.GKPNHADILLINL..VS.V.I.ND..ETP
Retrocopy KYFNIGSQGSCLKCQE*WLQGKVVAFNYQSTLLTLQGASSGGKPNHADILLINLEHVSDVAIMNDHPETP

Parental  PPLASLNVSKLASKARTEKEEKLSQAYA-ISAGVSLEGQQLFQTIH-KTIKDCKWQEKNIVVMEEVVITP
          .PLASL.VSKLASKART.K.EKLSQAY..IS.GVSLEGQQLFQ.I..KTIKDCKWQEK.I.VMEE.VITP
Retrocopy APLASLSVSKLASKART-KKEKLSQAYE<ISSGVSLEGQQLFQIIR>KTIKDCKWQEKSIIVMEEAVITP

Parental  PYQV-ENCKGKEG-SALSHVRKIVEKHFRDV
          ........K.K.G...LSHV.K.VEKHFRDV
Retrocopy ISSI<KSVKAKRG<CTLSHVHKTVEKHFRDV

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_3062 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3062 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 18 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014379	2 retrocopies	retro_cfam_1843, retro_cfam_312,
Choloepus hoffmanni	ENSCHOG00000001198	1 retrocopy	retro_chof_1429,
Dipodomys ordii	ENSDORG00000016381	1 retrocopy	retro_dord_596,
Erinaceus europaeus	ENSEEUG00000002419	1 retrocopy	retro_eeur_603,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Felis catus	ENSFCAG00000029083	1 retrocopy	retro_fcat_787,
Homo sapiens	ENSG00000161654	1 retrocopy	retro_hsap_4041,
Loxodonta africana	ENSLAFG00000005202	1 retrocopy	retro_lafr_906,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Myotis lucifugus	ENSMLUG00000006391	1 retrocopy	retro_mluc_2205,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3,
Mus musculus	ENSMUSG00000020922	1 retrocopy	retro_mmus_2683,
Otolemur garnettii	ENSOGAG00000010489	2 retrocopies	retro_ogar_1771, retro_ogar_2447,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12,
Pteropus vampyrus	ENSPVAG00000013706	1 retrocopy	retro_pvam_172,
Rattus norvegicus	ENSRNOG00000020894	1 retrocopy	retro_rnor_2845,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062 , retro_tbel_60,
Vicugna pacos	ENSVPAG00000011145	1 retrocopy	retro_vpac_627,