RetrogeneDB ID: retro_cjac_761

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:15816406..15816934(-)
• Located in intron of: ENSCJAG00000017991

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS15
• Ensembl ID: ENSCJAG00000001852
• Aliases: None
• Description: mitochondrial ribosomal protein S15 [Source:HGNC Symbol;Acc:14504]

Sequence

>retro_cjac_761
CTGAGGGCCACATGGAGAATGCCAAGTTCTATTTGGCCCTAGGCAGTGACCCAGACCCCAGTCCTTGGGCTGCCAGGCTA
AGGAAATGCCAGGCTTCCTTCCAACTGAAGGGGCCTGCAGTCTCAAAGTCTCCTCTAGGCTGCAGCACACATGCTATTTA
GAAACCAGTCTGGCTGAGACAGGACCATGACCAGCCCCCTTCCATGCTGCTCGAAGACCACCAAACCATCCCTGGAATTG
AGAAAGGCAATAATACAGTGAAAAGATCCTAATCTTTGGAAATGACCAACCAGAAGGAGAAGCTAAATATCATGCGAGAA
CATTTGATGAACCAAGTCATGGCAAACCTAAGGACACCAGCTTCCTGGAGGTTCAAATTAGTCCCTTGAGCAAAGTCCAC
GATTATGAAGAACACGTACAGAAACACTGGAAGGACAAAGCCCACAAATACTATTTGGTGATGAGCACTGTACAGAGGAA
AAGACACTCCAAAAACCTTTGTTAAGCCAATATGATGTCTCTGAGAAG

Alignment

ORF - retro_cjac_761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.8 %
• Parental protein coverage: 69.53 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LRAAWRMLSLIRTQAVTQAPGPGLPSCGSARFPSNQWGLQPRSLLQATRR-YVIQKPVLPRQDDDPPPST
          LRA.WRM.S.I...AVTQ.P..GLP..G.AR.PSN..GLQ..SLL.A......I.KPV..RQD.D.PPS.
Retrocopy LRATWRMPSSIWP*AVTQTPVLGLPG*GNARLPSN*RGLQSQSLL*AAAH<HAI*KPVWLRQDHDQPPSM

Parental  LLQDYQNVPGIEKVDDVVKRLLSLEMAKKKEKLKVIQEQLMKKIVEN-PEDTRSLEARIVALTIKIRSYE
          LL.D.Q..PGIEK....VKR..SLEM...KEKL....E.LM.....N.P.DT..LE..I..L..K...YE
Retrocopy LLEDHQTIPGIEKGNNTVKRS*SLEMTNQKEKLNIMREHLMNQVMAN<PKDTSFLEVQISPLS-KVHDYE

Parental  EHMQKHRKDKAHKRYLLMSIDQRKKMLKNLRNTN-YDVYEK
          EH.QKH.KDKAHK.YL.MS..QRK...KNL...N.YDV.EK
Retrocopy EHVQKHWKDKAHKYYLVMSTVQRKRHSKNLC*AN<YDVSEK

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	3.62 RPM
SRP051959_heart	0.00 RPM	7.33 RPM
SRP051959_kidney	0.00 RPM	6.68 RPM
SRP051959_liver	0.00 RPM	5.63 RPM
SRP051959_lung	0.00 RPM	5.32 RPM
SRP051959_lymph_node	0.00 RPM	4.89 RPM
SRP051959_skeletal_muscle	0.00 RPM	14.70 RPM
SRP051959_spleen	0.00 RPM	7.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_761 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_761 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_761 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1594
Pan troglodytes	retro_ptro_1071
Pongo abelii	retro_pabe_1310

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001463	1 retrocopy	retro_amel_1564,
Canis familiaris	ENSCAFG00000030390	1 retrocopy	retro_cfam_1939,
Callithrix jacchus	ENSCJAG00000001852	3 retrocopies	retro_cjac_3095, retro_cjac_761 , retro_cjac_859,
Cavia porcellus	ENSCPOG00000010877	1 retrocopy	retro_cpor_430,
Dipodomys ordii	ENSDORG00000007581	1 retrocopy	retro_dord_118,
Felis catus	ENSFCAG00000005265	1 retrocopy	retro_fcat_915,
Homo sapiens	ENSG00000116898	1 retrocopy	retro_hsap_1594,
Myotis lucifugus	ENSMLUG00000006475	1 retrocopy	retro_mluc_1945,
Monodelphis domestica	ENSMODG00000017813	1 retrocopy	retro_mdom_1094,
Mus musculus	ENSMUSG00000028861	1 retrocopy	retro_mmus_3447,
Nomascus leucogenys	ENSNLEG00000011467	1 retrocopy	retro_nleu_615,
Otolemur garnettii	ENSOGAG00000002656	2 retrocopies	retro_ogar_1327, retro_ogar_16,
Pongo abelii	ENSPPYG00000001537	1 retrocopy	retro_pabe_1310,
Pan troglodytes	ENSPTRG00000000541	1 retrocopy	retro_ptro_1071,
Sus scrofa	ENSSSCG00000026393	1 retrocopy	retro_sscr_1190,
Ictidomys tridecemlineatus	ENSSTOG00000000608	1 retrocopy	retro_itri_454,
Tupaia belangeri	ENSTBEG00000000958	4 retrocopies	retro_tbel_1633, retro_tbel_4438, retro_tbel_845, retro_tbel_882,
Tarsius syrichta	ENSTSYG00000008948	2 retrocopies	retro_tsyr_1612, retro_tsyr_372,
Tursiops truncatus	ENSTTRG00000002345	1 retrocopy	retro_ttru_1500,