RetrogeneDB ID: retro_cjac_2964

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:17378899..17380437(-)
• Located in intron of: ENSCJAG00000008267

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA7
• Ensembl ID: ENSCJAG00000015943
• Aliases: None
• Description: Importin subunit alpha [Source:UniProtKB/TrEMBL;Acc:F7I329]

Sequence

>retro_cjac_2964
ATGCTGAGCTTAGATGCTCCAGAAGAGAGGCTGAGAAAATTTAAGTACCGAGGCAAAGATGCATCTCTGAGGCGACAGCA
GAGGATGGCAGCCAGCCTGAAGCCCTGAAAGGCTGAGAAAGATGAACAGACCTTAAAGAGAAGGAATATCACCAGCTTCT
GCCCTGACACACCTTCTGAAAAAACAGCCAAAGGGGTGGCGGTCAGCCTCACTCTGGGTGAAATAATCCAAGGTGTGAAT
AGCTCAGATCCAGCCCTGTGTTTCCAGGCCACCCAGACAGCCAGAAAAATGCTATCGCAGGAAAAGAACTCCCCTCTGAA
ATTGGTCGTCCAAGCGGGCCTCATTCTCAGGATGGTGGAGTTCCTGAAGTCATCTCTTTCCCTCTTCTTGCAGTTAAAGG
CCTCCTGGGCCCTCACCAACATTGCTGCAGGGACTTCGGAGCAGACTCGAGCTGTGGTAGAAGGGGGAGCCATCCAGCCC
TTGATCGCGCTCCTGTCTCTCCCCAACCTGGCTGTGTGTGAACAGGCAGTGTGGGCTCTTGGTGGTAACATAGCTGGTGA
TGGCCCAGAGTTCAGAGATAAGATCATCTCAAGCAATGGTATCCCACATCTGCTGGCCTTGATTTCACACACCCTCCAAT
CACATTCCTGCAGAATATCACGTGGACCTTATCGAACCTTTGCGGAAACAAGAACCCGTACCCTTGCGATACTGCGGTGA
AGCAGATACTGCCGTCCCTCCTCCACCTCCGACAGCACCATGACAGTGAGGTTCTCTCCGACGCCTGCTGGCACTACCTC
ACTGACAGCTGCAGCAAGCGCATCGGACAAGTGTTTGACACGGGATTCCTGCCCTGGCTGGTGGCGCTCTTGATCAGCTT
AGAGCTCAACGTCTTGACCCCTTCTCTCCGCTCCGTGGGGAACATTGTCATGGGCACAGATGAACAGACGCAGAGAGCCA
TAGACACGGTCATACTGAACGTGCTCCCCTAGCTCCTCCAGCACAACAAGCCCTCTATTCAGAAGGAGGCAGCCTGGGCC
CTGAGCAACGTGGCGGCAGGACCCTGTCACCACATCCAGAAGCTGCTTGCCTACAACGTCTTGCCTCTCTTGGTGGCTGT
GCTAAAACATGGAGAATTTAAAGTCCAGAAAGAGGCTATCTGGACAGTGGCAAACTTTGTAACGGGGCCACCATGGTTCA
GCTGATCCAGCTCGTCCATTCTGGGATCCTGGATCCCCTGGTGAATCTGCTCACCTCCCGAGATGTTAAAATTGTTCATC
ATCCTCGATGTCATCTCTTTCATCCTCAAGGTGGCAGAGAAACTGTCTGAGAAGGAAAACGTGTGTCTTCTGATAGAAGA
ACTCGGTGGAATTGATAGAATTGAAGCTTTACAACTGCATGAGAACCGTCAGATTAGCCTGTCAGCTTTGAACATCATGG
AGAAGCACTTTAGCGAGGAAGAAGAGAGCCTAATGTTACTGAGCCAAGTCGTAGACCAAGATTGTGAATTTATAAACAGT
GACTGCTTAGCAAAAAAA

Alignment

ORF - retro_cjac_2964 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPSLDAPEERLRKFKYRGKDASLRRQQRMAVSLKLRKAKKDEQTLKRRNITSFCPDTPSEKTAKGVTVSL
          M.SLDAPEERLRKFKYRGKDASLRRQQRMA.SLK..KA.KDEQTLKRRNITSFCPDTPSEKTAKGV.VSL
Retrocopy MLSLDAPEERLRKFKYRGKDASLRRQQRMAASLKP*KAEKDEQTLKRRNITSFCPDTPSEKTAKGVAVSL

Parental  TLGEIIQGVNSSDPALCFQATQTARKMLSQENNPPLKLVVDAGLIPRMVEFLKSSLYPCLQFEAAWALTN
          TLGEIIQGVNSSDPALCFQATQTARKMLSQE.N.PLKLVV.AGLI.RMVEFLKSSL...LQ..A.WALTN
Retrocopy TLGEIIQGVNSSDPALCFQATQTARKMLSQEKNSPLKLVVQAGLILRMVEFLKSSLSLFLQLKASWALTN

Parental  IAAGTSEQTRAVVEGGAIQPLIALLSSPNLAVCEQAVWAL-GNIAGDGPEFRDKIISSNAIPHLLALISH
          IAAGTSEQTRAVVEGGAIQPLIALLS.PNLAVCEQAVWAL.GNIAGDGPEFRDKIISSN.IPHLLALISH
Retrocopy IAAGTSEQTRAVVEGGAIQPLIALLSLPNLAVCEQAVWALGGNIAGDGPEFRDKIISSNGIPHLLALISH

Parental  TL-PVSIFFFLFIFLXXXCRNKNPDPCDAAVKQILPALLHLLQHHDTEVLSDACWALSYLTDSCSKRIGQ
          TL.P..........L...C.NKNP.PCD.AVKQILP.LLHL.QHHD.EVLSDACW...YLTDSCSKRIGQ
Retrocopy TL<PITFLQNITWTLSNLCGNKNPYPCDTAVKQILPSLLHLRQHHDSEVLSDACW--HYLTDSCSKRIGQ

Parental  VVDTGVLPRLVALLNSSELNVLTPSLRTVGNIVTGTDEQTQRAIDTGILNVLPQLLQHNKPSIQKEAAWA
          V.DTG.LP.LVALL.S.ELNVLTPSLR.VGNIV.GTDEQTQRAIDT.ILNVLP.LLQHNKPSIQKEAAWA
Retrocopy VFDTGFLPWLVALLISLELNVLTPSLRSVGNIVMGTDEQTQRAIDTVILNVLP*LLQHNKPSIQKEAAWA

Parental  LSNVAAGPCHHIQQLLAYDVLPPLVAVLKHGDFKVQKEAIWTVANFVM-GATLDQLIQLVHSGILEPLVN
          LSNVAAGPCHHIQ.LLAY.VLP.LVAVLKHG.FKVQKEAIWTVANFV..GAT..QLIQLVHSGIL.PLVN
Retrocopy LSNVAAGPCHHIQKLLAYNVLPLLVAVLKHGEFKVQKEAIWTVANFVT<GATMVQLIQLVHSGILDPLVN

Parental  LLTAPDVKIV-LIILDVISFILEAAEKLSEKENVCLLIEELGGIDRIEALQLHENRQISLSALNIIEKHF
          LLT..DVKIV..I..DVISFIL..AEKLSEKENVCLLIEELGGIDRIEALQLHENRQISLSALNI.EKHF
Retrocopy LLTSRDVKIV>IIL-DVISFILKVAEKLSEKENVCLLIEELGGIDRIEALQLHENRQISLSALNIMEKHF

Parental  SEKEEESLMLLSQVVDQDCEFINCDCLATK
          SE.EEESLMLLSQVVDQDCEFIN.DCLA.K
Retrocopy SE-EEESLMLLSQVVDQDCEFINSDCLAKK

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
SRP051959_colon	0.00 RPM	0.02 RPM
SRP051959_heart	0.00 RPM	0.00 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.00 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.05 RPM
SRP051959_lymph_node	0.00 RPM	0.02 RPM
SRP051959_skeletal_muscle	0.02 RPM	0.00 RPM
SRP051959_spleen	0.00 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2964 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2964 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2964 has 0 orthologous retrocopies within eutheria group .

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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,