RetrogeneDB ID: retro_mmus_2844

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:82887822..82888720(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Kpna7
• Ensembl ID: ENSMUSG00000038770
• Aliases: Kpna7, AW146299, Gm1055
• Description: karyopherin alpha 7 (importin alpha 8) [Source:MGI Symbol;Acc:MGI:2141165]

Sequence

>retro_mmus_2844
ATGGCTACCTCAGAGGCTCCCAAGAGAAGCTGAAGAAATTTAAGTACCGAGGCAAAGAAATGTCTTTGCAGCAGCAACAG
AGGATTGCTTCCAGCCTACAACTCTGGAAGACTAGGAAATATAAGCAGGTGCTAAAGAGAAGAAATATCGATCTATTCTT
CAGTGACATGGTTTCTCAAGCACTAGTCAAAAAGGCCAACTTCACTCTGGACGACATCATCCAAGGGGTGAATAGTTTGG
ATATGATGCTGCGTTTCCAGGCCACCAAGGCTGCCAGGGAAATGCTATCTCAGGAAAATAACCCTCCTCTAAATTTGATT
ATTGAGGCCAGGCCCATCCCCAAGCTGGTAGATGTCCTGAAGGCGACACCTTTCCACAACCTGTAGTTCGAGGCGGCATG
GGCACTCACTAAACCACCTCAGAAACTGCAGAGCAGACCCAAGCTGTTATGAAAGGGGGTACCACTCAGCCCCTGATTGA
ACTCCTCTGTTCCCCTCACCTGACTGTGTCTGAGCAGGCAGTGTGGGTCCTTGGGAATATCGCTGGTGACTGTGCAGAAT
TCAGAGACAATGTCATTTCCAATACTGCCATCCCGCACCTGATCAACCTTATTTCAAAAAACATACTAGTCACATCTCTT
CGGAACGTCACATGGACTTTGGCCAACTTATGCCGAAACTAAGATCCACATCCTTATGAGGAGGCACTGAGGCAGATGCT
AGCGACCCTCTGTCAGCTCCCGCTGCATCATGATAATGAGATTCTTTCAGATATCTGCTGGGCCCTGGCCTACCTGACTG
AGGGTAGCAAAGAGTTCGTCCATCACGTGGTGACCACCGACATCCTGCCCGGGCTTGTAGAACTTAGGACCGGCTCAGAA
CTCAGTGCCTTGTCTCCA

Alignment

ORF - retro_mmus_2844 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.52 %
• Parental protein coverage: 60.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MATSKAPK-ERLKNYKYRGKEMSLPRQQRIASSLQLRKTRKDEQVLKRRNIDLFSSDMVSQALVKEVNFT
          MATS.APK.E.LK..KYRGKEMSL..QQRIASSLQL.KTRK..QVLKRRNIDLF.SDMVSQALVK..NFT
Retrocopy MATSEAPK<EKLKKFKYRGKEMSLQQQQRIASSLQLWKTRKYKQVLKRRNIDLFFSDMVSQALVKKANFT

Parental  LDDIIQAVNSSDPILHFRATRAAREMISQENTPPLNLIIEAGLIPKLVDFLKATPHPKLQFEAAWVLTN-
          LDDIIQ.VNS.D..L.................PPLNLIIEA..IPKLVD.LKATP...L.FEAAW.LT..
Retrocopy LDDIIQGVNSLDMMLRXXXXXXXXXXXXXXXXPPLNLIIEARPIPKLVDVLKATPFHNL*FEAAWALTK<

Parental  IASGTSEQTRAVVKEGAIQPLIELLCSPHLTVSEQAVWALGNIAGDCAEFRDCVISNNAIPHLINLISKG
          ..S.T.EQT.AV.K.G..QPLIELLCSPHLTVSEQAVW.LGNIAGDCAEFRD.VISN.AIPHLINLISK.
Retrocopy TTSETAEQTQAVMKGGTTQPLIELLCSPHLTVSEQAVWVLGNIAGDCAEFRDNVISNTAIPHLINLISKN

Parental  IPITFLRNISWTLSNLCRNKDPYPSESAVRQMLPPLCQLLLHRDNEILADTCWALSYLTKGGKEYIHHVV
          I..T.LRN..WTL.NLCRN.DP.P.E.A.RQML..LCQL.LH.DNEIL.D.CWAL.YLT.G.KE..HHVV
Retrocopy ILVTSLRNVTWTLANLCRN*DPHPYEEALRQMLATLCQLPLHHDNEILSDICWALAYLTEGSKEFVHHVV

Parental  TTGILPRLVELMTSSELSISIP
          TT.ILP.LVEL.T.SELS...P
Retrocopy TTDILPGLVELRTGSELSALSP

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	0.00 RPM	0.02 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.02 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	2.93 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2844 was not detected

EST

No EST(s) were mapped for retro_mmus_2844 retrocopy.

TSS

No TSS is located nearby retro_mmus_2844 retrocopy 5' end.

Lab

retro_mmus_2844 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2844 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 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	ENSMUSG00000018362	1 retrocopy	retro_mmus_229,
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,