RetrogeneDB ID: retro_cjac_4094

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:81261673..81262818(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000003671
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TFDP1
• Ensembl ID: ENSCJAG00000006950
• Aliases: None
• Description: transcription factor Dp-1 [Source:HGNC Symbol;Acc:11749]

Sequence

>retro_cjac_4094
GGCATGGTGTCCCTCGAGGCTGTTCACCCCTTCACAGTCAACCTGCTCGGGAAGCAGCTCTTGCCAAAAAACTTTGAAGA
GTCCAATGTCAACATTGCTCAGCATGTGGTAGTTGGTACTCTTCAGAGACCGGCAGCATCAAACACCCTCGTGGCAGGAC
GCCCACACACCCCAAGTACTCATTTGCCTCTCAGAACCAGTCTTCGGACTCCTCACCTTGGTCTGCCGGCAAGCACAACA
GGAAAGGAGAGAAGAAAGGCAAGGGCCTGCAGCATTTCTCCATGAAGTTCTACAAGGTACAGAGGAAACGGACCATTTCC
TACAACGAAGTGGCGGATGAGCTGGTCACGGAGTTCAGCGCTGCCGACAACCACATCTTACCAAAGGAGTCATCTTATGA
CCAGGAGAACATAAGACAGCATGTCTACAATACTTTAAATGTGCTGATGGCCATGAACATCATCTCCAAGAAGAAGGAGA
TCAGATTGATTAGTCTGTCCACCACCTCGGCTCAGGAATGTCAGAACTTAGAGGTGGAAAGACAGAGTAGACTTGAAAGT
ATAAAACACAAACAGTCTCGACTTCAAGAACTTATTCTATAGCAAATTGTCTTCAAGAACCTGATGCAGAGAAATCGACA
CGCTGAGGAGTAGGCTAGCTGGCTGCTACTGCCCAACTCAAACATCCATCTGCCCTTCATAATCGTCAACACCAGCAAGT
AGACTGTCATCGACTGTAGCATCTACAATGACAAATTCGAGTATATGTTTAATTTTGACAACACATTAGAAATCCACAAC
GACATAGACGTGCTGAAGTGGATGGGCATGGTGTGTAGGCTGTAGTCCGGAAGCTGCTCTGCTAAAGACCTTAAAATGAC
CAGAAGTCTGGTCCCTAAGGCTCTGGAGCCCTACGTGACAGAAATAACTCAGGGAAATGTTGGAGGCATGTTCATCACTA
CTGCAGGTTCCACGTCTAATGGCACGAGGTTCTCTGCCAGTGGCCTGACCAATGGTGCAGATGGGATGCTGGCCAAGAGC
TCCAAAGGGTCTCAGTACAGCAGCTCCAGGGTGGAGACCCCGGTGTCCTATGTCAGGGAAGACGTTGAAGATGATGATGA
CTTCAATGAGAATGATGAGGATGAC

Alignment

ORF - retro_cjac_4094 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.06 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GVVSLVAVHPSTVNPLGKQLLPKTFGQSNVNIAQQVVIGTPQRPAASNTLVVGSPHTPSTH-FASQNQPS
          G.VSL.AVHP.TVN.LGKQLLPK.F..SNVNIAQ.VV.GT.QRPAASNTLV.G.PHTPSTH.FASQNQ.S
Retrocopy GMVSLEAVHPFTVNLLGKQLLPKNFEESNVNIAQHVVVGTLQRPAASNTLVAGRPHTPSTH<FASQNQSS

Parental  DSSPWSAGKRNRKGEKNGKGLRHFSMKVCEKLHERGAPLSQCTWPTVSGSFGSFGNHSLHPQA-YDQKNI
          DSSPWSAGK.NRKGEK.GKGL.HFSMK.......R...........V...F....NH.L.....YDQ.NI
Retrocopy DSSPWSAGKHNRKGEKKGKGLQHFSMKFYKVQRKRTISYNEVADELVT-EFSAADNHILPKESSYDQENI

Parental  RRRVYDALNVLMAMNIISKEKKEIKWIGLPTNSAQECQNLEVERQRRLERIKQKQSQLQELILQQIAFKN
          R..VY..LNVLMAMNIISK.KKEI..I.L.T.SAQECQNLEVERQ.RLE.IK.KQS.LQELIL.QI.FKN
Retrocopy RQHVYNTLNVLMAMNIISK-KKEIRLISLSTTSAQECQNLEVERQSRLESIKHKQSRLQELIL*QIVFKN

Parental  LVQRNRHAEQQASRPPPPNSVIHLPFIIVNTSKKTVIDCSISNDKFEYLFNFDNTFEIHDDIEVLKRMGM
          L.QRNRHAE..AS....PNS.IHLPFIIVNTSK.TVIDCSI.NDKFEY.FNFDNT.EIH.DI.VLK.MGM
Retrocopy LMQRNRHAEE*ASWLLLPNSNIHLPFIIVNTSK*TVIDCSIYNDKFEYMFNFDNTLEIHNDIDVLKWMGM

Parental  ACGLESGSCSAEDLKMARSLVPKALEPYVTEMAQG-TGGVFITTAGSTSNGTRFSASDLTNGADGMLATS
          .C.L.SGSCSA.DLKM.RSLVPKALEPYVTE..QG..GG.FITTAGSTSNGTRFSAS.LTNGADGMLA.S
Retrocopy VCRL*SGSCSAKDLKMTRSLVPKALEPYVTEITQGNVGGMFITTAGSTSNGTRFSASGLTNGADGMLAKS

Parental  SNGSQYSGSRVETPVSYVGEDDEDDDDFNENDEDD
          S.GSQYS.SRVETPVSYV.ED.EDDDDFNENDEDD
Retrocopy SKGSQYSSSRVETPVSYVREDVEDDDDFNENDEDD

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	0.07 RPM	13.02 RPM
SRP051959_heart	0.05 RPM	9.00 RPM
SRP051959_kidney	0.02 RPM	11.47 RPM
SRP051959_liver	0.00 RPM	19.73 RPM
SRP051959_lung	0.02 RPM	12.27 RPM
SRP051959_lymph_node	0.05 RPM	18.86 RPM
SRP051959_skeletal_muscle	0.00 RPM	8.63 RPM
SRP051959_spleen	0.00 RPM	13.34 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4094 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4094 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4094 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004467	8 retrocopies	retro_chof_2187, retro_chof_2229, retro_chof_2621, retro_chof_506, retro_chof_529, retro_chof_837, retro_chof_854, retro_chof_895,
Callithrix jacchus	ENSCJAG00000001950	1 retrocopy	retro_cjac_3164,
Callithrix jacchus	ENSCJAG00000006950	2 retrocopies	retro_cjac_179, retro_cjac_4094 ,
Homo sapiens	ENSG00000198176	4 retrocopies	retro_hsap_1601, retro_hsap_299, retro_hsap_4803, retro_hsap_61,
Gorilla gorilla	ENSGGOG00000004908	2 retrocopies	retro_ggor_17, retro_ggor_335,
Loxodonta africana	ENSLAFG00000007927	1 retrocopy	retro_lafr_914,
Myotis lucifugus	ENSMLUG00000012165	1 retrocopy	retro_mluc_896,
Macaca mulatta	ENSMMUG00000007423	1 retrocopy	retro_mmul_177,
Mus musculus	ENSMUSG00000038482	2 retrocopies	retro_mmus_3243, retro_mmus_338,
Nomascus leucogenys	ENSNLEG00000000849	3 retrocopies	retro_nleu_2177, retro_nleu_2598, retro_nleu_49,
Otolemur garnettii	ENSOGAG00000003532	1 retrocopy	retro_ogar_3334,
Pongo abelii	ENSPPYG00000025889	3 retrocopies	retro_pabe_1314, retro_pabe_132, retro_pabe_378,