RetrogeneDB ID: retro_tbel_3962

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_45611:181..1048(+)
• 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_3962
CCCCCCATGGACAATATCATCCGGGCTGGGTTGATTCCAAAATTTGTGTCCTTCTTGGGCAGAAATGATTATAGTCCCAT
CCAGTTTGAATCTGCATGGGCACTCACTAACATTGCTTCTGGGACGTCAGAACAGACAAAGGCTGTGCTGGATGGAGGCA
CTATCCCAGCATTCATTTCTCTGTTGGCCTCTCCCCATGCGCACATCAGTGAGCAAGCTGTGTGGACTCTAGAAAACATC
GCAGGGGATGGTTCAGTTTTCTGGGACCTGGTTATCAAGTATGGAGCAATTGACCCGCTGTTGGCTCTCCTTGCAGTTCC
TGATAGGTCATCGTTAGCATGTGGTTACTTACATAACCTTACCTGGACACTTTCAAACCTCTGTCGCAAGAAGAATCCCG
CACCCCCGCTAGATGCTGTTGAGCAGATTCTTCCTACTTTAGTTCATCTTCTGCATCACGATGATCCCGAAGTATTAGCA
TATACCTGCTGGGCCATTTCCTACCTTACTGATGGTCCAAATGAACGGATTAAAATGGTTGTGAAAACAGGAATTGTTCC
CCAACTTGTGAAGCTTCTAGGCGCTACTGAATTGCCCATTGTGACCCCTGCCCTAAGAGCCATAGGTAATATTGTCACTG
GGACAGATGAACAGACCCAGGTTGTGATAGATGCTGGAGCACTCGCCATCTTCCCCAGCCTTCTAACCAACTCCAAAACA
AATATTCAGAAGGAAAATACTTGGACCATGTCCAACATCACCGCCGGTCGGCAGAACCAGATCCAGCAGGTTGTGAATCA
TGGGTTAGTCCCGTTCCTGGTCAGCGTGCTCTCCAAGGCTGACTTTAAGACATAGAAGGAGGCTGTG

Alignment

ORF - retro_tbel_3962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.36 %
• Parental protein coverage: 58.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPLKLIIEAGLIPRLVEFLKSSLHPCLQFEAAWALTNIASGTSEQTRAVVEGGAIQPLIKLLSSPNVTVC
          PP...II.AGLIP..V.FL........QFE.AWALTNIASGTSEQT.AV..GG.I...I.LL.SP.....
Retrocopy PPMDNIIRAGLIPKFVSFLGRNDYSPIQFESAWALTNIASGTSEQTKAVLDGGTIPAFISLLASPHAHIS

Parental  EQAVWALGNIAGDGPEFRDIIISSNAIPHLLALVS----STLPITFLRNITWTLSNLCRNKNPYPCDKAV
          EQAVW.L.NIAGDG..F.D..I...AI..LLAL......S.L....L.N.TWTLSNLCR.KNP.P...AV
Retrocopy EQAVWTLENIAGDGSVFWDLVIKYGAIDPLLALLAVPDRSSLACGYLHNLTWTLSNLCRKKNPAPPLDAV

Parental  KQMLPVLSYLLQHQDSEIVSDTCWALSYLTDGSNERIGHVVDMGVLPRLVELLASSELNVLTPSLRTVGN
          .Q.LP.L..LL.H.D.E....TCWA.SYLTDG.NERI..VV..G..P.LV.LL...EL...TP.LR..GN
Retrocopy EQILPTLVHLLHHDDPEVLAYTCWAISYLTDGPNERIKMVVKTGIVPQLVKLLGATELPIVTPALRAIGN

Parental  IVTGTDHQTQMAIDAGMLSLLPQLLGHPKPSIQKEAAWALSNVAAGPCHHIQQLISYDMLPPLVALLKNG
          IVTGTD.QTQ..IDAG.L...P.LL...K..IQKE..W..SN..AG....IQQ.......P.LV..L...
Retrocopy IVTGTDEQTQVVIDAGALAIFPSLLTNSKTNIQKENTWTMSNITAGRQNQIQQVVNHGLVPFLVSVLSKA

Parental  DFKVQKEAV
          DFK..KEAV
Retrocopy DFKT*KEAV

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_3962 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_3962 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,