RetrogeneDB ID: retro_cjac_1176

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:4496384..4497267(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGPAT9
• Ensembl ID: ENSCJAG00000005314
• Aliases: None
• Description: None

Sequence

>retro_cjac_1176
CAACTCACTATGGTGTGGGTGCTGGGCATCATAGTGCGCTATTGTGTCCTACTGCCTCTGAGGGTTACCTTGGCTTTCAT
TTGTATCAGTTTGCTGGTTATAGGAACTACACTGGTTGGGAAGCTGCCAGATATGGCCTCAAAAACTGGCTGAGTGAACT
GGTCCATCTGACTTGCTACCGGATCTGTGTTCGAGCCCTCTCTGGTACCATTCATTATCATAACAAGCAGTACAGATCCC
AGAAGGGAGGCATTTGTGTTGCCAACCATACTTCCCCAATTGATGTTTTAATCTTGACAACAGATGGATGTTATGCTATG
GTTGCCCAGGTTCATGGTGGCTTGATGGGAATTACTCAGAGAGCTATGATCAAGCCTTGTCCTCATGTCTGGTTTGAATG
CTCAGAAATGAAATATCAACACCTGGTTACTAAGAGACCAAAAGAACATATTGCTGATAAGAAGAAATTACCCATATTAA
TTTTTCCTGAAGGAACCTGCATCAACAATACTTCAGTCATGCTGTTTAAAAAGGGGAGCTTTGAAATTGGAGGAACCATA
CATCCAGTTGCAATTAAGTCTAACCCTCAGTTTGGTGATGCATTTTGGAACAGTAGAAAGTACAACATGGTCAGCTACCT
GCTGTGAATGATGACCAGCTGGGCCATCGTCTGTGACGTGTGGTACATGCCCCCATGACCAGAGAGGAAGGAGAAGATGC
AGTCCAGTTTGCCAACAGGGTTAAGTCTGCTACTGCTATACAAGGAGGCCTGACTGAACTTCCCTGGGATGGAGGGCTAA
AGAGAGCAAAAATGAAGGACACCTTCAAGGAAGAGCAGCAGATAAATTATAGCAAGATGATTGTGGGCAATGGGTCTCTC
AAC

Alignment

ORF - retro_cjac_1176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.91 %
• Parental protein coverage: 67.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RLTMVWVLGVIVRYCVLLPLRVTLAFIGISLLVIGTTLVGQLPDSS-LKNWLSELVHLTCCRICVRALSG
          .LTMVWVLG.IVRYCVLLPLRVTLAFI.ISLLVIGTTLVG.LPD...LKNWLSELVHLTC.RICVRALSG
Retrocopy QLTMVWVLGIIVRYCVLLPLRVTLAFICISLLVIGTTLVGKLPDMA<LKNWLSELVHLTCYRICVRALSG

Parental  TIHYHNKQYRPQKGGICVANHTSPIDVLILTTDGCYAMVGQVHGGLMGIIQRAMVKACPHVWFERSEMKD
          TIHYHNKQYR.QKGGICVANHTSPIDVLILTTDGCYAMV.QVHGGLMGI.QRAM.K.CPHVWFE.SEMK.
Retrocopy TIHYHNKQYRSQKGGICVANHTSPIDVLILTTDGCYAMVAQVHGGLMGITQRAMIKPCPHVWFECSEMKY

Parental  RHLVTKRLKEHIADKKKLPILIFPEGTCINNTSVMMFKKGSFEIGGTIHPVAIKYNPQFGDAFWNSSKYN
          .HLVTKR.KEHIADKKKLPILIFPEGTCINNTSVM.FKKGSFEIGGTIHPVAIK.NPQFGDAFWNS.KYN
Retrocopy QHLVTKRPKEHIADKKKLPILIFPEGTCINNTSVMLFKKGSFEIGGTIHPVAIKSNPQFGDAFWNSRKYN

Parental  MVSYLLRMMTSWAIVCDVWYMP-PMTREVGEDAVQFANRVKSAIARQGGLTELPWDGGLKRAKVKDTFKE
          MVSYLL.MMTSWAIVCDVWYMP.PMTRE.GEDAVQFANRVKSA.A.QGGLTELPWDGGLKRAK.KDTFKE
Retrocopy MVSYLL*MMTSWAIVCDVWYMP<PMTREEGEDAVQFANRVKSATAIQGGLTELPWDGGLKRAKMKDTFKE

Parental  EQQKNYSKMIVGNGSLN
          EQQ.NYSKMIVGNGSLN
Retrocopy EQQINYSKMIVGNGSLN

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	26.49 RPM
SRP051959_heart	0.02 RPM	60.15 RPM
SRP051959_kidney	0.07 RPM	118.05 RPM
SRP051959_liver	0.00 RPM	5.65 RPM
SRP051959_lung	0.00 RPM	6.07 RPM
SRP051959_lymph_node	0.00 RPM	2.08 RPM
SRP051959_skeletal_muscle	0.02 RPM	101.94 RPM
SRP051959_spleen	0.00 RPM	5.63 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1176 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1176 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1176 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005314	1 retrocopy	retro_cjac_1176 ,
Monodelphis domestica	ENSMODG00000020776	1 retrocopy	retro_mdom_94,