RetrogeneDB ID: retro_cjac_2417

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:24007848..24009151(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC1
• Ensembl ID: ENSCJAG00000017701
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 1 [Source:HGNC Symbol;Acc:9547]

Sequence

>retro_cjac_2417
GGTCAAAGTCAGAGTAGTGGCAGTGGTTGTGGAGATGGCAAGAAGGATGACAAGGACAAGAAAAGGAAATATGAACCTCC
TGTAGCAACTAAGGTGGGGACAAAGAAGAAAACCAAGAGACCAGATTCCGCCAGCAAACTGCCACTGGTGACACCTAACA
CTTGGTGCTGGTTAAAATTACTGAAGTTAGAGAGAATTAAAGACTGTCTTCTCATGGAGGAAGAATTCATTAGAAATCGG
GAACAAGTGAAACCATTAGAAGAAAAGCAAGAGGAGAACAGATCATAAACGGATGATCTGAGGGGGACCCCAATGACAGT
AGGAACCTTGCAAGAGATCATCGATGACAATCATGCCATCGCGTCTACAACTGTAGGCTCAGAACACTACGTCAGCATTC
TTTCATTTGTAGAAAAGGATCCGCTGGAAGCTGGTGGCTCAGTCCTGCTCAGCTACAAGGAGCATGCCATGATAGGGGTG
CTGATGGATAACACAGATCTCCTGGTCACAATGAAGGTGGAAAAGGCTCCCCAGGAGACCTATGCTGATATTGGGGAGTT
TGACAACCAAATTCAGGAAATTAAGGAATCTTTGGAGCTTCCTCTCACCCATCCTGAATATTATGAAGAGATGGGTATAC
AGCCTCCTAAGGAGGTCATTGTCTATGGCCCACCAGGCACAGGTAAAACCTTGTTAGCCAAAGCAGTAGCAAACCAAACC
TCAGCCACTTTCTTGAGAGTGGTTGGCTCTGAACTTACTCAGAAGTACCTAGGTGTAGGCCCAAACTTGTACGGGAATTA
TTTTGAGTTGCTGAAGAACATGCACCATCCATTATGTTTATTGATGAAATTAACGCCATTGGGACAAAAAGATATGACTC
AAATTCTGGTAGAGAAATTCAGAGAACATTGTTGGAACTGTTGAACCAGTTGGATGAATTTGATTCTGGAAGAGGTGTGA
AAGTTATCATGGCCACAAACCAGATAGAAACTTTGGATCCAGCACTTATCAAACCAGGCTGCATCGACAGGAAGATTGAG
TTCCCCCTGCCTGATGGAAAGACTAAGACGTGCATCTTTCAGATTCACAAAAGCAGGATGACGCTGGCCGATGATGTAAC
CCGGGACAACGTGATTATAGCTAAAGATGATCTCTCTGGTGCTGACATCAAGGCAATCTGTACAGGAGCTGGTCTGATGG
CCTTCAGAGAACGTAGAATGAAAGTAACAAATGAAGACTTCAAAAATCTGAAGAAAATATTCTTTATAAGAAACAGGAAG
GCACCCCTGTGGGGCTCTATCTC

Alignment

ORF - retro_cjac_2417 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.9 %
• Parental protein coverage: 99.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GQSQSGGHGPGGGKKDDKDKKKKYEPPVPTRVGKKKKKTKGPDAASKLPLVTPHTQCRLKLLKLERIKDY
          GQSQS.G.G.G.GKKDDKDKK.KYEPPV.T.VG.KKK.TK.PD.ASKLPLVTP.T.C.LKLLKLERIKD.
Retrocopy GQSQSSGSGCGDGKKDDKDKKRKYEPPVATKVGTKKK-TKRPDSASKLPLVTPNTWCWLKLLKLERIKDC

Parental  LLMEEEFIRNQEQMKPLEEKQEEERSKVDDLRGTPMSVGTLEEIIDDNHAIVSTSVGSEHYVSILSFVDK
          LLMEEEFIRN.EQ.KPLEEKQEE.RS..DDLRGTPM.VGTL.EIIDDNHAI.ST.VGSEHYVSILSFV.K
Retrocopy LLMEEEFIRNREQVKPLEEKQEENRS*TDDLRGTPMTVGTLQEIIDDNHAIASTTVGSEHYVSILSFVEK

Parental  DLLEPGCSVLLNHKVHAVIGVLMDDTDPLVTVMKVEKAPQETYADIGGLDNQIQEIKESVELPLTHPEYY
          D.LE.G.SVLL..K.HA.IGVLMD.TD.LVT.MKVEKAPQETYADIG..DNQIQEIKES.ELPLTHPEYY
Retrocopy DPLEAGGSVLLSYKEHAMIGVLMDNTDLLVT-MKVEKAPQETYADIGEFDNQIQEIKESLELPLTHPEYY

Parental  EEMGIKPPKGVILYGPPGTGKTLLAKAVANQTSATFLRVVGSELIQKYLGDG-PKLVRELFRVAEEHAPS
          EEMGI.PPK.VI.YGPPGTGKTLLAKAVANQTSATFLRVVGSEL.QKYLG.G.PKLVRELF.VAEEHAPS
Retrocopy EEMGIQPPKEVIVYGPPGTGKTLLAKAVANQTSATFLRVVGSELTQKYLGVG<PKLVRELF*VAEEHAPS

Parental  IVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDSRGDVKVIMATNRIETLDPALIRPGRIDRK
          I.FIDEI.AIGTKRYDSNSG..REIQRT.LELLNQLD.FDS...VKVIMATN.IETLDPALI.PG.IDRK
Retrocopy IMFIDEINAIGTKRYDSNSG--REIQRTLLELLNQLDEFDSGRGVKVIMATNQIETLDPALIKPGCIDRK

Parental  IEFPLPDEKTKKRIFQIHTSRMTLADDVTLDDLIMAKDDLSGADIKAICTEAGLMALRERRMKVTNEDFK
          IEFPLPD.KTK..IFQIH.SRMTLADDVT.D..I.AKDDLSGADIKAICT.AGLMA.RERRMKVTNEDFK
Retrocopy IEFPLPDGKTKTCIFQIHKSRMTLADDVTRDNVIIAKDDLSGADIKAICTGAGLMAFRERRMKVTNEDFK

Parental  -KSKENVLYKKQEGTPEGLYL
          .KS.EN.LYKKQEGTP.GLYL
Retrocopy <KSEENILYKKQEGTPVGLYL

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	22.32 RPM
SRP051959_heart	0.00 RPM	26.31 RPM
SRP051959_kidney	0.04 RPM	27.04 RPM
SRP051959_liver	0.00 RPM	29.85 RPM
SRP051959_lung	0.00 RPM	19.50 RPM
SRP051959_lymph_node	0.00 RPM	18.06 RPM
SRP051959_skeletal_muscle	0.02 RPM	57.61 RPM
SRP051959_spleen	0.02 RPM	22.48 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2417 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2417 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2417 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017510	2 retrocopies	retro_cfam_1238, retro_cfam_1562,
Choloepus hoffmanni	ENSCHOG00000013595	1 retrocopy	retro_chof_1954,
Callithrix jacchus	ENSCJAG00000017701	7 retrocopies	retro_cjac_1152, retro_cjac_1537, retro_cjac_2417 , retro_cjac_2433, retro_cjac_4219, retro_cjac_661, retro_cjac_678,
Dasypus novemcinctus	ENSDNOG00000006458	1 retrocopy	retro_dnov_2162,
Homo sapiens	ENSG00000100764	10 retrocopies	retro_hsap_1090, retro_hsap_1278, retro_hsap_2080, retro_hsap_2658, retro_hsap_2810, retro_hsap_2873, retro_hsap_3323, retro_hsap_3416, retro_hsap_3793, retro_hsap_975,
Gorilla gorilla	ENSGGOG00000010620	8 retrocopies	retro_ggor_1004, retro_ggor_1298, retro_ggor_1629, retro_ggor_1954, retro_ggor_1993, retro_ggor_2309, retro_ggor_780, retro_ggor_858,
Macropus eugenii	ENSMEUG00000001526	1 retrocopy	retro_meug_623,
Microcebus murinus	ENSMICG00000016733	7 retrocopies	retro_mmur_1039, retro_mmur_1063, retro_mmur_1245, retro_mmur_1577, retro_mmur_216, retro_mmur_839, retro_mmur_983,
Macaca mulatta	ENSMMUG00000022990	1 retrocopy	retro_mmul_255,
Nomascus leucogenys	ENSNLEG00000017013	10 retrocopies	retro_nleu_1123, retro_nleu_1163, retro_nleu_1589, retro_nleu_1625, retro_nleu_1669, retro_nleu_2318, retro_nleu_2625, retro_nleu_429, retro_nleu_616, retro_nleu_706,
Oryctolagus cuniculus	ENSOCUG00000006231	4 retrocopies	retro_ocun_1135, retro_ocun_1212, retro_ocun_1654, retro_ocun_411,
Otolemur garnettii	ENSOGAG00000032343	2 retrocopies	retro_ogar_3014, retro_ogar_367,
Pongo abelii	ENSPPYG00000025948	9 retrocopies	retro_pabe_1059, retro_pabe_153, retro_pabe_2379, retro_pabe_2408, retro_pabe_2737, retro_pabe_2832, retro_pabe_3099, retro_pabe_825, retro_pabe_907,
Pan troglodytes	ENSPTRG00000006623	9 retrocopies	retro_ptro_1530, retro_ptro_1904, retro_ptro_1944, retro_ptro_2153, retro_ptro_2321, retro_ptro_2573, retro_ptro_672, retro_ptro_742, retro_ptro_874,