RetrogeneDB ID: retro_cjac_1520

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:68394259..68395206(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD7
• Ensembl ID: ENSCJAG00000015129
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 [Source:HGNC Symbol;Acc:9565]

Sequence

>retro_cjac_1520
ATGTGACAGCTGGCGGTGCAGATAGTGGTGGTCCACACCCTGGTGCTGCTCAGTGTGGTGGTTCATTTCAACCGAATCAG
AAAGGCTGGAAATCAGAAGCGCATTGTTGGTGTGCTTTTGGGGTCATAAGAAAAGAAAGTACTTGATGTATTGAACACTT
TTGCAGTTCCTTTTGGTAAAGATGACCAAGATGATTCTGTGTGGTTTTTAGACCATGATTATTTGGAAAACATGCATGGA
ATGTTCAAGAAAGTCAATGCCAGAGAAAGAATAGTGGGCTGGTACCACACAGACCCTAAACTACACAAGAATGACATTAC
CATCAATGAACTAATGAAAAGATACTGTCCTAATTCCGTATTGGTCATTACTGACATGAAGCCAAAGGACTTAGGGCGGC
CCACAGAAGTGTACATTTCAGTGGAAGAAGTCCATAATGACAGAATGCCAACCTCGAAAACATTTGAACATGTGACCAGT
GAAATTGGAGCTGAGAAAGTTGGAGTTGGACACTTGTTACGAGGCACCAAAGACACGATGGCGGGCACTTTGTCCCAACG
GATCACAAATCAGGTCCATGGTTTGAAGGAACTGAACTCCAATCTTCTGGATATCAGGAGCTACCTGGAAAAAAGTAGCC
TCAGGCAAGCTGCCTATCCAACCACCGGATCATCTACCAGCTGCAGGACATCATCAACCTGTGCCAGATGTCAGCCTGCA
GGAGTTTGTCAAAGCCTTTTATCTGACGACCAACCGACCAGATGGGGGTAGTGTACTTGGCTTCATTGATCCTTTCCGCG
GTCACCCTGCTCAACCTCAACAACGAGATTGCCAACTGGGATGCAGAGAAGAAAGAAGGGTAGGAGAAAGAAGAGAACAA
AAAGGATAGGAAAGAGGACACGGAGAAAGATAAAGATAAGGAAGACTGATGTAAAGAGCAGAAAAAG

Alignment

ORF - retro_cjac_1520 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.92 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPELAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVWFL
          M..LAVQ.VVVH.LVLLSVV.HFNRI.K.GNQKR.VGVLLGS..KKVLDV.N.FAVPF..DD.DDSVWFL
Retrocopy M*QLAVQIVVVHTLVLLSVVVHFNRIRKAGNQKRIVGVLLGS*EKKVLDVLNTFAVPFGKDDQDDSVWFL

Parental  DHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPKDLGLPTEAYIS
          DHDYLENM.GMFKKVNARERIVGWYHT.PKLHKNDI.INELMKRYCPNSVLVI.D.KPKDLG.PTE.YIS
Retrocopy DHDYLENMHGMFKKVNARERIVGWYHTDPKLHKNDITINELMKRYCPNSVLVITDMKPKDLGRPTEVYIS

Parental  VEEVHDDGTPTSKTFEHVTSEIGAEEAEEVGVEHLLRDIKDTTVGTLSQRITNQVHGLKGLNSKLLDIRS
          VEEVH.D..PTSKTFEHVTSEIGAE....VGV.HLLR..KDT..GTLSQRITNQVHGLK.LNS.LLDIRS
Retrocopy VEEVHNDRMPTSKTFEHVTSEIGAE---KVGVGHLLRGTKDTMAGTLSQRITNQVHGLKELNSNLLDIRS

Parental  YLE-KVATGKLPI-NHQIIYQLQDVFNL-LPDVSLQEFVKAFYLKTN-DQMVVVYLASLIRSVVALHNLI
          YLE.KVA.GKLPI.NH.IIYQLQD..NL..PDVSLQEFVKAFYL.TN.DQM.VVYLASLI.S.V.L.NL.
Retrocopy YLE>KVASGKLPI>NHRIIYQLQDIINL<VPDVSLQEFVKAFYLTTN>DQMGVVYLASLILSAVTLLNL-

Parental  NNKIANRDAEKKEGQEKEESKKDRKEDKEKDKDKEKSDGKKEEKK
          NN.IAN.DAEKKEG.EKEE.KKDRKED.EKDKDKE..D..KE.KK
Retrocopy NNEIANWDAEKKEG*EKEENKKDRKEDTEKDKDKE--D*CKEQKK

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	21.79 RPM
SRP051959_heart	0.00 RPM	23.57 RPM
SRP051959_kidney	0.00 RPM	22.54 RPM
SRP051959_liver	0.00 RPM	22.87 RPM
SRP051959_lung	0.03 RPM	21.99 RPM
SRP051959_lymph_node	0.00 RPM	26.46 RPM
SRP051959_skeletal_muscle	0.00 RPM	40.53 RPM
SRP051959_spleen	0.00 RPM	25.95 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1520 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1520 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1520 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Callithrix jacchus	ENSCJAG00000015129	2 retrocopies	retro_cjac_1520 , retro_cjac_2910,
Homo sapiens	ENSG00000103035	2 retrocopies	retro_hsap_1781, retro_hsap_234,
Gorilla gorilla	ENSGGOG00000009774	1 retrocopy	retro_ggor_2235,
Myotis lucifugus	ENSMLUG00000005416	1 retrocopy	retro_mluc_505,
Macaca mulatta	ENSMMUG00000011125	4 retrocopies	retro_mmul_1242, retro_mmul_372, retro_mmul_417, retro_mmul_566,
Nomascus leucogenys	ENSNLEG00000005608	1 retrocopy	retro_nleu_1310,
Otolemur garnettii	ENSOGAG00000014868	1 retrocopy	retro_ogar_388,
Procavia capensis	ENSPCAG00000014356	1 retrocopy	retro_pcap_399,
Pongo abelii	ENSPPYG00000025918	1 retrocopy	retro_pabe_418,
Pan troglodytes	ENSPTRG00000008343	2 retrocopies	retro_ptro_1192, retro_ptro_205,
Tupaia belangeri	ENSTBEG00000016950	1 retrocopy	retro_tbel_4135,