RetrogeneDB ID: retro_cjac_3284

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:24370558..24371300(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011697
• Aliases: None
• Description: None

Sequence

>retro_cjac_3284
ATGATGGGGATCATGCTCACACAGACTGCGTAGTGCAGGAACCAGATTAGCACCAAGTTCTGGGTGGTGATCTCTGATGA
ACATGCCATCGACTCAGCTGGCACCTCCTATGAGGCCAGCAATCTGCAGCTGGAGCACATCAATGTGTACTACAATGAGG
CCAGCAGTGGCAGGTACATGCATTGTGCTGTGCTTATGGATCTGGAGTCAGGCACTATGGACACTGTGCACTAGGGGCCC
TTTGGGCGGATCTTCAGGCCAGACAACTTCATCTTCAGTCAGTGTGGGGCTGGGAACAACTGGGCCAAGGGGCACTACAC
AGAGGTGTGGAGCTGATGGAGTCAGTGATGGACGTATTGAGGAAGGAGGCTGAGAGCTGTGACTGCCTGTAGAGTTTCCA
ACTGAGCTACTTCCTGGGTGGGGGGACTGAGTCTGGTATGGATACCCTTCTCATCAGTAAAATCTGGGAGGAGTACCCAG
ACAGGATCATAAACACATTCAGTGTCCTGCTCTGGCCCAAGGTGTCAGACACTGTGGTGGAGCCCTACAATGCCACCCTC
TCAGTCCACCAGCTCATAGAAAATACAGATGAGACATTTTGCATTGATATGAAGTTCTGTATAACATCTGTGCCAGAACT
CTGAAACTGCCCACACCCACTTGTGGTGACCTGAATCACCTGGTGTCTAATACCATGAATGGGGTCACCATGTGCCTGTG
CTTCCCAGGCCAGCTGAATGCT

Alignment

ORF - retro_cjac_3284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.0 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MREIVLTQTGQCGNQIGAKFWEVISDEHGIDPAGTYHGDSDLQLERINVYYNEASGGRYVARAVLVDLEP
          M..I.LTQT..C.NQI..KFW.VISDEH.ID.AGT....S.LQLE.INVYYNEAS.GRY...AVL.DLE.
Retrocopy MMGIMLTQTA*CRNQISTKFWVVISDEHAIDSAGTSYEASNLQLEHINVYYNEASSGRYMHCAVLMDLES

Parental  GTMDSVRSGPFGKIFRPDNFIFGQCGAGNNWAKGYYTE-GAELMESVMDVVRKEAESCDCLQGFQLTHSL
          GTMD.V..GPFG.IFRPDNFIF.QCGAGNNWAKG.YTE.G.ELMESVMDV.RKEAESCDCL..FQL...L
Retrocopy GTMDTVH*GPFGRIFRPDNFIFSQCGAGNNWAKGHYTE<GVELMESVMDVLRKEAESCDCL*SFQLSYFL

Parental  GGGTGSGMGTLLTGKIREEYPDRIINTFSVLPSPKVSDTVVEPYNATLSVHQLIENADETFCID-NEALY
          GGGT.SGM.TLL..KI.EEYPDRIINTFSVL..PKVSDTVVEPYNATLSVHQLIEN.DETFCID..E.LY
Retrocopy GGGTESGMDTLLISKIWEEYPDRIINTFSVLLWPKVSDTVVEPYNATLSVHQLIENTDETFCID<YEVLY

Parental  NICSRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNA
          NIC.RTLKL.TPT.GDLNHLVS.TM.GVT.CL.FPGQLNA
Retrocopy NICARTLKLPTPTCGDLNHLVSNTMNGVTMCLCFPGQLNA

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	0.04 RPM
SRP051959_heart	0.04 RPM	0.02 RPM
SRP051959_kidney	0.00 RPM	0.00 RPM
SRP051959_liver	0.11 RPM	0.00 RPM
SRP051959_lung	0.00 RPM	0.00 RPM
SRP051959_lymph_node	0.11 RPM	0.00 RPM
SRP051959_skeletal_muscle	0.94 RPM	0.00 RPM
SRP051959_spleen	0.06 RPM	0.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3284 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3284 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3284 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004826	2 retrocopies	retro_cjac_1632, retro_cjac_2667,
Callithrix jacchus	ENSCJAG00000010101	1 retrocopy	retro_cjac_800,
Callithrix jacchus	ENSCJAG00000010530	1 retrocopy	retro_cjac_1144,
Callithrix jacchus	ENSCJAG00000011697	1 retrocopy	retro_cjac_3284 ,
Callithrix jacchus	ENSCJAG00000017637	1 retrocopy	retro_cjac_1649,
Dipodomys ordii	ENSDORG00000015889	1 retrocopy	retro_dord_254,
Homo sapiens	ENSG00000173213	1 retrocopy	retro_hsap_3733,
Homo sapiens	ENSG00000173876	1 retrocopy	retro_hsap_3944,
Mus musculus	ENSMUSG00000016255	1 retrocopy	retro_mmus_1109,
Pongo abelii	ENSPPYG00000011180	1 retrocopy	retro_pabe_3250,