RetrogeneDB ID: retro_cjac_2190

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:141714378..141715161(+)
• Located in intron of: ENSCJAG00000018615

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPI1
• Ensembl ID: ENSCJAG00000007348
• Aliases: None
• Description: triosephosphate isomerase 1 [Source:HGNC Symbol;Acc:12009]

Sequence

>retro_cjac_2190
GACACTGACCTTCAGTGCTTTGGCTTCAGCGCCATGGTACCCTCCAGGAAGTTCTTTGTGGGGAGGGAACTGGAAGCTGA
ATGCGGGGAAGAAGAGTCTGGGAGAGCTTATCCACACTCTGAATTCAGCCAAGGTGCCGGCAGACACTAAGGTGGTTTGC
GCTCCCCCAACTGCCTATATCAACTTCGCCCAGCAGAAGCTAGATTCCAAGATTGCTGTGGCTTCGTAGAACTGCTACAA
AGTGACTAATGGAGACTTTTCTGGGGAGATCAGCCCTGGCGTGATCAAAGACTGCAGAGCCACATGGGTTGTCCTGGGGC
ACTGAGAGAGAAGGCATGCCTTTGGGGAGTCAGATGAGCTGATTGGGCAGAAAGTGGCCCATGCTCTGGAAGAGGCACTC
AGAGCAATTGCCTGCATTGGGGAGAAGCTAGATGATAAGGAAGCTGGCATCACTAAGAAGGTTTTTTTCGAGCAGACAAA
GGTCATCACAGATAATGTGAAGGACTAGAGCAAGGTCATCCTGGCCTATGAGCCTGTGTGGGCCATTGGTACTGGCAAGA
CTGTAACACCCCAGCAAGCCCAGGGAGTACACAAGAAGCTCGAGGATGGCTTAAGTCCAATGTCTCTGATGCAATGGCTC
AGAGCACCCATACATATCATTTATGAGGCTCTGTGACCAGGGCAACCTGCAAGGGGCTGGCCAGCCAGCCTGATGTAGAT
GGCTTCCTCATGGGTAGTGCTTCCCTTAAGCTCAAATTTATGGATATCATCAATGTCAAACAA

Alignment

ORF - retro_cjac_2190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.09 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DTDLQCLGSSAMAPSRKFFVG-GNWKMNGRKQNLGELIGTLNAAKVPGDTEVVCAPPTAYIDFARQKLDP
          DTDLQC.G.SAM.PSRKFFVG.GNWK.N..K..LGELI.TLN.AKVP.DT.VVCAPPTAYI.FA.QKLD.
Retrocopy DTDLQCFGFSAMVPSRKFFVG>GNWKLNAGKKSLGELIHTLNSAKVPADTKVVCAPPTAYINFAQQKLDS

Parental  KIAVAAQNCYKVSNGAFTGEISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALAEGLGVIACI
          KIAVA..NCYKV.NG.F.GEISPG.IKDC.ATWVVLGH.ERRH.FGESDELIGQKVAHAL.E.L..IACI
Retrocopy KIAVAS*NCYKVTNGDFSGEISPGVIKDCRATWVVLGH*ERRHAFGESDELIGQKVAHALEEALRAIACI

Parental  GEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKL-RGWLKSNV
          GEKLD..EAGIT.KV.FEQTKVI.DNVKD.SKV.LAYEPVWAIGTGKT.TPQQAQ.VH.KL.RGWLKSNV
Retrocopy GEKLDDKEAGITKKVFFEQTKVITDNVKD*SKVILAYEPVWAIGTGKTVTPQQAQGVHKKL<RGWLKSNV

Parental  SDAVAQSTRIIY-GGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ
          SDA.AQST......GSVT.ATCK.LASQPDVDGFL.G.ASLK..F.DIIN.KQ
Retrocopy SDAMAQSTHTYHL*GSVTRATCKGLASQPDVDGFLMGSASLKLKFMDIINVKQ

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	1.80 RPM	70.80 RPM
SRP051959_heart	0.11 RPM	75.42 RPM
SRP051959_kidney	0.42 RPM	79.87 RPM
SRP051959_liver	0.06 RPM	82.57 RPM
SRP051959_lung	0.07 RPM	32.81 RPM
SRP051959_lymph_node	0.05 RPM	41.23 RPM
SRP051959_skeletal_muscle	0.50 RPM	236.59 RPM
SRP051959_spleen	0.02 RPM	41.51 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2190 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2190 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2190 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3038
Pan troglodytes	retro_ptro_1999

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007348	2 retrocopies	retro_cjac_2190 , retro_cjac_2370,
Homo sapiens	ENSG00000111669	3 retrocopies	retro_hsap_3038, retro_hsap_3510, retro_hsap_3784,
Gorilla gorilla	ENSGGOG00000002623	1 retrocopy	retro_ggor_151,
Macropus eugenii	ENSMEUG00000006977	5 retrocopies	retro_meug_1348, retro_meug_1520, retro_meug_1934, retro_meug_267, retro_meug_512,
Myotis lucifugus	ENSMLUG00000024989	4 retrocopies	retro_mluc_1090, retro_mluc_1311, retro_mluc_1777, retro_mluc_1807,
Macaca mulatta	ENSMMUG00000005194	2 retrocopies	retro_mmul_1864, retro_mmul_250,
Mustela putorius furo	ENSMPUG00000016774	1 retrocopy	retro_mputfur_136,
Mus musculus	ENSMUSG00000023456	4 retrocopies	retro_mmus_1180, retro_mmus_3260, retro_mmus_532, retro_mmus_558,
Nomascus leucogenys	ENSNLEG00000004821	2 retrocopies	retro_nleu_1120, retro_nleu_847,
Otolemur garnettii	ENSOGAG00000031254	1 retrocopy	retro_ogar_109,
Pongo abelii	ENSPPYG00000004207	1 retrocopy	retro_pabe_2902,
Pan troglodytes	ENSPTRG00000004595	4 retrocopies	retro_ptro_160, retro_ptro_1999, retro_ptro_2382, retro_ptro_2565,
Rattus norvegicus	ENSRNOG00000015290	1 retrocopy	retro_rnor_1304,
Rattus norvegicus	ENSRNOG00000050669	2 retrocopies	retro_rnor_2615, retro_rnor_787,