RetrogeneDB ID: retro_cjac_2370

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:115923056..115923841(+)
• Located in intron of: ENSCJAG00000004595

Retrocopy information

• Ensembl ID: ENSCJAG00000031350
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2370
GACACTGACCTTCAGCGCCTCGGCTCCAATGCCATGGCGCCCTCCAGGAAGCTCTTCATGGGTAGCGGGGTAGGGAACTG
GAAGATGAACAGGCAGAAGAAGAGTCTGGGAGAGCTCATCTGCACTCTGAACGCGGCCAAGATGTCCGCTGACACCAAGT
GGTTTGGGCTCCCCCCGCTGCCTATATTGACTTTGCCCGGCAGAAACTACATCCCAAAATTGCTGTGGCTGTGTGGAACT
GCTACAAAGTGACTAACGAGGCCTTCACTGGGAGATCAGCCCTGGCATGATCAAAAACTGCAGAGCCACGTGGGTGGTCC
TGGGGCACTCAGAGAGAAAGCATGTCTTTGGGAAGTCAGATGAGCTGGTTGGGCAGAAAGTGGTCCATCCTCCAGCAGAG
GGACTCGGAGTAATCGCCTGCGTTGGGGAGCAGCTAGATGAAAGGGAAGCTGGCATCATTAAGAAGGTTGCTTTCAAGCA
GACAAAGGTAATCGCAGATAACATGAAGGATTGGAACTGGGTCGTCCTGGACTGTGAGCCTGTGTGGACCATTGGTACCG
GCAAGACTGCAACACCCAACAGGCCCAGGAAGTACACGACAAGTTCAAGGATGGCTTAAGTCCAACGTCTCTGATGCAGT
AGCTCCGAGCACCTGTATCATTTTTGGAGGCTGTGTGACTGGGGCAATCTGCAAGGGGCTGGCCAGCCAGCCTGATGTGG
ATGGCTTCCTCATGGGTGGTGCTTCCCTCAAGCCCGAATTCGTGAACATCATCAATGCCAAACAA

Alignment

ORF - retro_cjac_2370 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.28 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DTDLQCLGSSAMAPSRKFFVG---GNWKMNGRKQNLGELIGTLNAAKVPGDT-EVVCAPPTAYIDFARQK
          DTDLQ.LGS.AMAPSRK.F.G...GNWKMN..K..LGELI.TLNAAK...DT..VV.APP.AYIDFARQK
Retrocopy DTDLQRLGSNAMAPSRKLFMGSGVGNWKMNRQKKSLGELICTLNAAKMSADT<QVVWAPPAAYIDFARQK

Parental  LDPKIAVAAQNCYKVSNGAFTG-EISPGMIKDCGATWVVLGHSERRHVFGESDELIGQKVAHALAEGLGV
          L.PKIAVA..NCYKV.N.AFTG.EISPGMIK.C.ATWVVLGHSER.HVFG.SDEL.GQKV.H..AEGLGV
Retrocopy LHPKIAVAVWNCYKVTNEAFTG<EISPGMIKNCRATWVVLGHSERKHVFGKSDELVGQKVVHPPAEGLGV

Parental  IACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATP-QQAQEVHEK-LRGW
          IAC.GE.LDEREAGI..KV.F.QTKVIADN.KDW..VVL..EPVW.IGTGKTATP.QQAQEVH.K...GW
Retrocopy IACVGEQLDEREAGIIKKVAFKQTKVIADNMKDWNWVVLDCEPVWTIGTGKTATP<QQAQEVHDK<VQGW

Parental  LKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ
          LKSNVSDAVA.ST.II.GG.VTGA.CK.LASQPDVDGFL.GGASLKPEFV.IINAKQ
Retrocopy LKSNVSDAVAPSTCIIFGGCVTGAICKGLASQPDVDGFLMGGASLKPEFVNIINAKQ

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	1.46 RPM	70.80 RPM
SRP051959_heart	0.00 RPM	75.42 RPM
SRP051959_kidney	1.00 RPM	79.87 RPM
SRP051959_liver	0.87 RPM	82.57 RPM
SRP051959_lung	0.33 RPM	32.81 RPM
SRP051959_lymph_node	0.05 RPM	41.23 RPM
SRP051959_skeletal_muscle	0.00 RPM	236.59 RPM
SRP051959_spleen	0.69 RPM	41.51 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2370 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2370 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2370 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3510
Pan troglodytes	retro_ptro_2382
Pongo abelii	retro_pabe_2902
Macaca mulatta	retro_mmul_1864

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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,