RetrogeneDB ID: retro_tbel_3862

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_24494:462..1205(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA7
• Ensembl ID: ENSTBEG00000009007
• Aliases: None
• Description: karyopherin alpha 7 (importin alpha 8) [Source:HGNC Symbol;Acc:21839]

Sequence

>retro_tbel_3862
ATCATCTGGGCTGGATTGATTCCAAAATTTGTGTCCTTTTTGGGCAGAAATGATTGTAGTCCTATCCAGTTTGAATCTGC
ATGGGCACTCACTAACATTGCTTCTGGGACGTCAGAACAGACCAAGGACGTGGTGGACGGAAGAGGTATCCCAGCGTTCA
TTTCTCTGTTGGCCTCTCCCCACGCACACATCAGTGAACAAGCTGTGTGGGCTCTAGGAAACACCGCAGGAGATGGTTCA
GTTTCCGGGACCTGGTTATCAAGTACGGAGCAGTTGACCCGCTATTGACTCTCCTTGCAGTTCCTGATATGTCATCGTTA
GCATGTGGTCACTTACATAACCTTACTTGGACACTTTCAAACCTCTGCTGCAACAAGAATCTTGCACCCCCGCTAGATGC
TGTTGAGCAGATTCTTCCTACTTTAATTTATCTTCTGCATCACGATGATCCAGAAGTATTAGCAGATACCTGCTGGGCTA
TTTCCTACCTTACTGATGGTTCAAATGAATGGATTGACATGGCTGTGAAAACAGGAGTTGTTTCCCAACTTGTGAAGCTT
CTAGGAGCTACCGAAGAGCCCATTGTGACTCCTGCCCTAAGAGCCATAGGTAATATTGTCACTGGGACAGACGAGCAGAC
TCAGGTTGTGATAGATGGTGGAGCACTCGCAGTCTTCCCTAGCCTGCTAACTAACTCCAAAACGAATATTCAGAAAGAAG
CTACATGGACAATGTCCAACATC

Alignment

ORF - retro_tbel_3862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.22 %
• Parental protein coverage: 50.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IIEAGLIPRLVEFLKSSLHPCLQFEAAWALTNIASGTSEQTRAVVEGGAIQPLIKLLSSPNVTVCEQAVW
          II.AGLIP..V.FL........QFE.AWALTNIASGTSEQT..VV.G..I...I.LL.SP.....EQAVW
Retrocopy IIWAGLIPKFVSFLGRNDCSPIQFESAWALTNIASGTSEQTKDVVDGRGIPAFISLLASPHAHISEQAVW

Parental  ALGNIAGDGP-EFRDIIISSNAIPHLLALVS----STLPITFLRNITWTLSNLCRNKNPYPCDKAVKQML
          ALGN.AGDG...FRD..I...A...LL.L......S.L....L.N.TWTLSNLC.NKN..P...AV.Q.L
Retrocopy ALGNTAGDGS<SFRDLVIKYGAVDPLLTLLAVPDMSSLACGHLHNLTWTLSNLCCNKNLAPPLDAVEQIL

Parental  PVLSYLLQHQDSEIVSDTCWALSYLTDGSNERIGHVVDMGVLPRLVELLASSELNVLTPSLRTVGNIVTG
          P.L.YLL.H.D.E...DTCWA.SYLTDGSNE.I...V..GV...LV.LL...E....TP.LR..GNIVTG
Retrocopy PTLIYLLHHDDPEVLADTCWAISYLTDGSNEWIDMAVKTGVVSQLVKLLGATEEPIVTPALRAIGNIVTG

Parental  TDHQTQMAIDAGMLSLLPQLLGHPKPSIQKEAAWALSNV
          TD.QTQ..ID.G.L...P.LL...K..IQKEA.W..SN.
Retrocopy TDEQTQVVIDGGALAVFPSLLTNSKTNIQKEATWTMSNI

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_3862 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3862 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 15 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015125	2 retrocopies	retro_cfam_459, retro_cfam_861,
Choloepus hoffmanni	ENSCHOG00000004243	1 retrocopy	retro_chof_805,
Callithrix jacchus	ENSCJAG00000015943	1 retrocopy	retro_cjac_2964,
Equus caballus	ENSECAG00000000554	1 retrocopy	retro_ecab_981,
Echinops telfairi	ENSETEG00000000096	1 retrocopy	retro_etel_1548,
Homo sapiens	ENSG00000185467	1 retrocopy	retro_hsap_3337,
Mus musculus	ENSMUSG00000038770	2 retrocopies	retro_mmus_2844, retro_mmus_3301,
Nomascus leucogenys	ENSNLEG00000010827	1 retrocopy	retro_nleu_1680,
Otolemur garnettii	ENSOGAG00000031106	3 retrocopies	retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps	ENSOPRG00000015434	2 retrocopies	retro_opri_1101, retro_opri_118,
Pongo abelii	ENSPPYG00000017369	1 retrocopy	retro_pabe_2750,
Pan troglodytes	ENSPTRG00000019446	2 retrocopies	retro_ptro_102, retro_ptro_2142,
Tupaia belangeri	ENSTBEG00000006274	14 retrocopies	retro_tbel_1635, retro_tbel_2077, retro_tbel_2672, retro_tbel_2792, retro_tbel_290, retro_tbel_3638, retro_tbel_4120, retro_tbel_4358, retro_tbel_4414, retro_tbel_4435, retro_tbel_4558, retro_tbel_810, retro_tbel_97, retro_tbel_976,
Tupaia belangeri	ENSTBEG00000009007	3 retrocopies	retro_tbel_1475, retro_tbel_3862 , retro_tbel_3962,
Tursiops truncatus	ENSTTRG00000002998	2 retrocopies	retro_ttru_1426, retro_ttru_430,