RetrogeneDB ID: retro_ptro_2142

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:39714203..39715693(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA7
• Ensembl ID: ENSPTRG00000019446
• Aliases: None
• Description: karyopherin alpha 7 (importin alpha 8) [Source:HGNC Symbol;Acc:21839]

Sequence

>retro_ptro_2142
TACTAAGGCAAAGATGCATCTCTGAGGCGACAGCAGAGGATAGCAGTCAGCCTGGAGCTCCGAAAGGCCAAGAAAGATGA
ACAGATCTTAAAGAGAAAGAATATCACCAGCTTCTGCCCTGATACAGCTTCCAAAAAACCAGCCAAAGGGGTGGCAGTCA
GCTTCACTCTGGTGAAATAATCAAAGGTGTGAATAGCTCAGATTCAGTCCCACGGTTCCAGGCCACCGAGACAGCCAGGA
AAATGCTATCCCAGGAAAAGAACCCCCTTCTGAAATTGAGCATTGAAGCAGGCTTCATTCGCAGGATGGTAGAGTTCCTG
AAGTCATCACTTTACCCCTGCTTGCAGTTTGAGGCCGCCTGGGCCCTGACCAACATTGCTTCAGGGACTTCCGAGCAGAT
TTGAGCCGTGGTAGAAGGGGGACCCATCCAGCCCTTGATCAAGCTCCTGTCTTCCCCCAACGTGGCTGTGTGTGAACAGG
CAATGTGGGCTCTTGGTAATATACCCGGTGACGGCCTGGAGTTCAGAGATAATGTCATTTCAAGCAATGCCATCCCACAT
CTGCGGGCCTTGATTTCACCCACCCTACCAATCACATTTCTGCGGAACATCACGTGGACCTTGTCGAACCTATGCCGAAA
AAAGACCCCGTACCCTTGCGAAACTGCAGTGAAGCAGATGCTGCGTGCCCTCTCACTCCTGCAGCGCCACCACAGCGAGG
TTCTCTCGGAAGCCTGCTGGTCACTGTCCTACCTCACCTACGGCTGCAAAGAGCTCATCGGCCAAGTGGATGACACAGGG
GTCCTGCTCAGACTAGTAGCCCTCATGACCATCTCAGAACTCAATGTCTGGACCCCTTCTCTCCCGTACCATGGGGAACA
TTATCACAGGCACAAATTAACAGAAGCAGATGGCCATTGACGCGGGCATGCTGAACGTGCTGCCCCAGTTCCTGCAGCAC
AACAAGCCCTCCATCCAGGAAGCGGCCTGGGCCCTGAGCAACGTGGCGGCAGGGCCCTCTCACCACACCCAGCAGCTGCT
TGCCTACAACGTCTTGCCTCCCGTGGTGGCTCTGCTAAAAAAAATGGAGAATTTAAAGTCCAGAAAGAGGCTGTCTGGAC
GGTGGCTAACTTTGCAATGTGGGTCACCGTGGATAAGTTGATCCTCCACTCTGGGGTCCTGGAGCCACTGATGAATCTGC
TCATTGCCCCAGATGTTAAAATTGTTCTCATCATTCTCGATGTAATCTCTTGCATCCTCCAGGCGGCAGAGAAACGGTCT
GAGAAGGAAATCCTATGTTTTCTGATAGAACAGCTCGGTGGGATCGATAGAATTGAGGCTTTACAACTGCATGAGAACTG
TCAGATTGGCCAGTCTGCTTTGAACATCATTGAGCAGCACTTTGGTGAGGAAGAAGATGAGAGTCTAACTTTACTGAGCC
AAGTCCTAGACCAAGATTGTGAATTTATAGATTGTGAATGCTTAGCAAAA

Alignment

ORF - retro_ptro_2142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.35 %
• Parental protein coverage: 96.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YRGKDASLRRQQRMAVSLELRKAKKDEQTLKRRNIMSFCPDTPSEKTAKGVAVSLTL-GEIIEGVNSSDP
          Y.GKDASLRRQQR.AVSLELRKAKKDEQ.LKR.NI.SFCPDT.S.K.AKGVAVS.TL.GEII.GVNSSD.
Retrocopy Y*GKDASLRRQQRIAVSLELRKAKKDEQILKRKNITSFCPDTASKKPAKGVAVSFTL<GEIIKGVNSSDS

Parental  VLCFQATQTARKMLSREKNPPLKLVIEAGLIPRMVEFLKSSLYPCLQFEAAWALTNIASGTSEQTRAVVE
          V..FQAT.TARKMLS.EKNP.LKL.IEAG.I.RMVEFLKSSLYPCLQFEAAWALTNIASGTSEQ..AVVE
Retrocopy VPRFQATETARKMLSQEKNPLLKLSIEAGFIRRMVEFLKSSLYPCLQFEAAWALTNIASGTSEQI*AVVE

Parental  GGAIQPLIELLSSSNVAVCEQAVWALGNIAGDGPEFRDNVITSNAIPHLLALISPTLPITFLRNITWTLS
          GG.IQPLI.LLSS.NVAVCEQA.WALGNI.GDG.EFRDNVI.SNAIPHL.ALISPTLPITFLRNITWTLS
Retrocopy GGPIQPLIKLLSSPNVAVCEQAMWALGNIPGDGLEFRDNVISSNAIPHLRALISPTLPITFLRNITWTLS

Parental  NLCRNKNPYPCDTAVKQILPALLHLLQHQDSEVLSDACWALSYLTDGSNKRIGQVVNTGVLPRLVVLMTS
          NLCR.K.PYPC.TAVKQ.L.A.L.LLQ...SEVLS.ACW.LSYLT.G....IGQV..TGVL.RLV.LMT.
Retrocopy NLCRKKTPYPCETAVKQMLRA-LSLLQRHHSEVLSEACWSLSYLTYGCKELIGQVDDTGVLLRLVALMTI

Parental  SELNVLTPSL-RTVGNIVTGTDEQTQMAIDAGMLNVLPQLLQHNKPSIQKEAAWALSNVAAGPCHHIQQL
          SELNV.TPSL.RT.GNI.TGT..Q.QMAIDAGMLNVLPQ.LQHNKPSIQ.EAAWALSNVAAGP.HH.QQL
Retrocopy SELNVWTPSL>RTMGNIITGTN*QKQMAIDAGMLNVLPQFLQHNKPSIQ-EAAWALSNVAAGPSHHTQQL

Parental  LAYDVLPPLVALLKNGE-FKVQK-EAVWTVANFATGATMDQLIQLVHSGVLEPLVNLLTAPDVKIVLIIL
          LAY.VLPP.VAL....E..K..K.EAVWTVANFA...T.D.LI...HSGVLEPL.NLL.APDVKIVLIIL
Retrocopy LAYNVLPPVVALXXXXENLKSRK<EAVWTVANFAMWVTVDKLI--LHSGVLEPLMNLLIAPDVKIVLIIL

Parental  DVISCILQAAEKRSEKENLCLLIEELGGIDRIEALQLHENRLIGQSALNIIEKHFGEEEDESQTLLSQVI
          DVISCILQAAEKRSEKE.LC.LIE.LGGIDRIEALQLHEN..IGQSALNIIE.HFGEEEDES.TLLSQV.
Retrocopy DVISCILQAAEKRSEKEILCFLIEQLGGIDRIEALQLHENCQIGQSALNIIEQHFGEEEDESLTLLSQVL

Parental  DQDYEFIDYECLAK
          DQD.EFID.ECLAK
Retrocopy DQDCEFIDCECLAK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.05 RPM
SRP007412_cerebellum	0.04 RPM	0.14 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.05 RPM
SRP007412_liver	0.00 RPM	0.07 RPM
SRP007412_testis	0.00 RPM	4.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2142 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2142 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2142 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3337
Pongo abelii	retro_pabe_2750

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 23 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	ENSTBEG00000009007	3 retrocopies	retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus	ENSTTRG00000002998	2 retrocopies	retro_ttru_1426, retro_ttru_430,