RetrogeneDB ID: retro_tbel_1708

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: GeneScaffold_5522:3341..3872(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTBEG00000009428
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTBEG00000005913
• Aliases: None
• Description: None

Sequence

>retro_tbel_1708
GACCAGATGTGGCGGCCAGTGGTGAGCATTTGATGCACCAGTGAGCAGCCCTATGTGGCTTTCACTGGTGTCATGGAGCA
GAAACTGCTTCCAAGCACGGTGAGGCCCATGGAAAGATCTGGAGCTGCTCCTGTGGGGTCCCACTACGCCTGATGGAGCC
CAACCACTTCTTCTACTATAACATCAGTCAGGATCGCAGGAGGCAGACCTCATGAGGATCAGCTGCCCTCCTACGAGAGT
CTGAAGGACATGATGGCCAGAGCTCTGCCCTTTGGAATGAAGAAATAGTTCCCCAGATCACGGATGGGAAACGGGCACTG
ACTGAGCCATGGCAACAGCTGTTGGGGGCATTGTCAACATCTGGAAGTTCTCAGAAGAGGCTGTTGGGGAACTGCACCTG
CCTGCTGGTATGCATATTGTCTCTGCATTAGGCAAGAACTTGAATCCCATCAAGCCCAGGCAGTTCCTGACAGATGAAGA
GACTGTGTGTAAAACCCTGGAAGCTGAGCTGCCCAGGGCGAGGCCAAGAAG

Alignment

ORF - retro_tbel_1708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.22 %
• Parental protein coverage: 86.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  DQMWLPVVRTWRLNERHYGGLTGLNK-AETAAKHGEAQVKIWRRSYDVPPP-MEPDHPFYSNISKDRRY-
          DQMW.PVV......E..Y...TG....AETA.KHGEA..KIW..S..VP...MEP.H.FY.NIS.DRR..
Retrocopy DQMWRPVVSI*CTSEQPYVAFTGVME<AETASKHGEAHGKIWSCSCGVPLRLMEPNHFFYYNISQDRRR<

Parental  ADLT-EDQLPSCESLKDTIARALPF-WNEEIVPQIKEGKRVLIA-AHGNSLRGIVKHLEGLSEEAIMELN
          ADL..EDQLPS.ESLKD..ARALPF.WNEEIVPQI..GKR.L...A......GIV......SEEA..EL.
Retrocopy ADLM<EDQLPSYESLKDMMARALPF<WNEEIVPQITDGKRALTE<AMATAVGGIV-NIWKFSEEAVGELH

Parental  LPTGIPIVYELDKNLKPIKPMQFLGDEETVRKAMEAV-AAQGKAKK
          LP.G..IV..L.KNL.PIKP.QFL.DEETV.K..EA..AAQG.AKK
Retrocopy LPAGMHIVSALGKNLNPIKPRQFLTDEETVCKTLEAE<AAQGEAKK

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_1708 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_1708 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 17 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012697	2 retrocopies	retro_btau_1611, retro_btau_472,
Canis familiaris	ENSCAFG00000009062	1 retrocopy	retro_cfam_1297,
Callithrix jacchus	ENSCJAG00000016575	1 retrocopy	retro_cjac_370,
Cavia porcellus	ENSCPOG00000006844	4 retrocopies	retro_cpor_158, retro_cpor_539, retro_cpor_605, retro_cpor_660,
Echinops telfairi	ENSETEG00000002467	1 retrocopy	retro_etel_1595,
Homo sapiens	ENSG00000171314	12 retrocopies	retro_hsap_1048, retro_hsap_1052, retro_hsap_1142, retro_hsap_2235, retro_hsap_2604, retro_hsap_3083, retro_hsap_3488, retro_hsap_4249, retro_hsap_4686, retro_hsap_4821, retro_hsap_885, retro_hsap_913,
Gorilla gorilla	ENSGGOG00000028602	13 retrocopies	retro_ggor_1220, retro_ggor_1500, retro_ggor_1667, retro_ggor_1824, retro_ggor_2061, retro_ggor_2118, retro_ggor_2353, retro_ggor_2849, retro_ggor_3005, retro_ggor_3034, retro_ggor_716, retro_ggor_738, retro_ggor_827,
Loxodonta africana	ENSLAFG00000015979	1 retrocopy	retro_lafr_886,
Microcebus murinus	ENSMICG00000007657	1 retrocopy	retro_mmur_135,
Macaca mulatta	ENSMMUG00000020027	1 retrocopy	retro_mmul_119,
Monodelphis domestica	ENSMODG00000004242	4 retrocopies	retro_mdom_1342, retro_mdom_1893, retro_mdom_610, retro_mdom_668,
Oryctolagus cuniculus	ENSOCUG00000005679	5 retrocopies	retro_ocun_1016, retro_ocun_1081, retro_ocun_350, retro_ocun_706, retro_ocun_976,
Pongo abelii	ENSPPYG00000002530	9 retrocopies	retro_pabe_1325, retro_pabe_2309, retro_pabe_2554, retro_pabe_2639, retro_pabe_2881, retro_pabe_3389, retro_pabe_3639, retro_pabe_3749, retro_pabe_671,
Rattus norvegicus	ENSRNOG00000050585	7 retrocopies	retro_rnor_1669, retro_rnor_2241, retro_rnor_2275, retro_rnor_2361, retro_rnor_2568, retro_rnor_691, retro_rnor_703,
Tupaia belangeri	ENSTBEG00000004587	1 retrocopy	retro_tbel_3939,
Tupaia belangeri	ENSTBEG00000005913	5 retrocopies	retro_tbel_1677, retro_tbel_1708 , retro_tbel_2756, retro_tbel_3667, retro_tbel_563,
Drosophila melanogaster	FBgn0014869	1 retrocopy	retro_dmel_57,