RetrogeneDB ID: retro_cjac_179

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:121090645..121091869(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022006
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

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_179
ATGGCAGAATATATCAGTATAGCGAAAGCTAACAAGGAACTCAAGGTCGTAATGGACCAGAACCAGACCAGTGGCCCCAT
GGAGGTTCAGCCCTACATCCTAAAGCCGTTTGGGAGGCCGTTCTTGCCAAAAACCTTTGGAGAGTCCACTGTCAACAATG
TGCAGCAAGTGGTAATTGGTATGCCTCAGAGACTGGCAACATCAAACATCCTTGTGGTAGGCAGCCCAAACCCACCCAGC
ACTCATTTTGCCTCTCAGAACCAGCCTTCCAACTCCTCACCTTGGTTGGCCAGGCAACGCTGCAAGAAAGTAGAGAAGGA
TGGCATAGGCCTGCAACATTTCTCCATGAAGGTCTGGGAGAAGGTGCAGAAGAAAGGGACCACTTCCTCTAAGGAAGTGG
TGGGTGAGCTGGTCACCGAGTTCAAAGCTGCCAACAACCACCTCCCACCACACGAGATAGCTTGTGACCTGAAGAACATA
AAACGGCGCGTCTATGATGCCTTAAACGTGCTGATGGCCATGAACATCATCTCCAGGGAGGGGAAGATGATCAAGTGGAT
TGGTCTGATTGGTCTGTCCACCACCTCGGCTCAGGACTATCAAAGCTTACAAGTGGAAAAAGAGAAAAGACTTGAAAGAA
TAAAGGAGAAAGAATCTCGACTTCAACAACTTATTCTACAGCAAATTGCCTTCAAGAACCTGGTGCAGAAAAACCGGTAT
GCAGAGGAACAGGGCAGCCAGCAGCTGCCGCCCAGCTCAGTCATCCACCTGCCCTTTGTGATTGTCAGCACCAGCAAGAA
TAGCGTCATCAACTGCAGCATCTCCAACGACGGATTTGATTATCTGTTTCATTTTGAAAACCCATTTGAAGTCCACGATT
ACACAGAAGTGCTGCAATGGATGGGCATGACTTTCGGGCTAGAGTCTGGGATCTGTTCTGCCAAAGACCTTAAAATGGCC
AGAAGTTTGGTCCCAAAGGCTCTGGAGCCATATGTGACAAAAATGGCTAACGGAACTTTTGGAGATATGTTCACGATGTC
AGGTTCCACGTCTAATGACATGCAGCTCTCTGCCAGTGATCTGACCAACACTGTAGATGGGATGCTGGCCACAAGCTCCA
GTGGGATTCAGTGCAGTGGCTTCAGGGTGGAGACCCCTGTGGTTGAGGAGGAGGAGGATGACAGCAAGAATAATGATTTC
AATGATGATGACAAGTATGACTGA

Alignment

ORF - retro_cjac_179 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.38 %
• Parental protein coverage: 98.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VHPSTVNPLGKQLLPKTFGQSNVNIAQQVVIGTPQRPAASNTLVVGSPHTPSTHFASQNQPSDSSPWSAG
          V.P....P.G...LPKTFG.S.VN..QQVVIG.PQR.A.SN.LVVGSP..PSTHFASQNQPS.SSPW.A.
Retrocopy VQPYILKPFGRPFLPKTFGESTVNNVQQVVIGMPQRLATSNILVVGSPNPPSTHFASQNQPSNSSPWLAR

Parental  KRNRKGEKNGKGLRHFSMKVCEKLHERGAPLSQCTWPTVSGSFGSFGNH-SLHPQAYDQKNIRRRVYDAL
          .R..K.EK.G.GL.HFSMKV.EK....G...S..........F....NH...H..A.D.KNI.RRVYDAL
Retrocopy QRCKKVEKDGIGLQHFSMKVWEKVQKKGTTSSKEVVGELVTEFKAANNHLPPHEIACDLKNIKRRVYDAL

Parental  NVLMAMNIISKEKKEIKW---IGLPTNSAQECQNLEVERQRRLERIKQKQSQLQELILQQIAFKNLVQRN
          NVLMAMNIIS.E.K.IKW...IGL.T.SAQ..Q.L.VE...RLERIK.K.S.LQ.LILQQIAFKNLVQ.N
Retrocopy NVLMAMNIISREGKMIKWIGLIGLSTTSAQDYQSLQVEKEKRLERIKEKESRLQQLILQQIAFKNLVQKN

Parental  RHAEQQASRPPPPNSVIHLPFIIVNTSKKTVIDCSISNDKFEYLFNFDNTFEIHDDIEVLKRMGMACGLE
          R.AE.Q.S...PP.SVIHLPF.IV.TSK..VI.CSISND.F.YLF.F.N.FE.HD..EVL..MGM..GLE
Retrocopy RYAEEQGSQQLPPSSVIHLPFVIVSTSKNSVINCSISNDGFDYLFHFENPFEVHDYTEVLQWMGMTFGLE

Parental  SGSCSAEDLKMARSLVPKALEPYVTEMAQGTGGVFITTAGSTSNGTRFSASDLTNGADGMLATSSNGSQY
          SG.CSA.DLKMARSLVPKALEPYVT.MA.GT.G...T..GSTSN....SASDLTN..DGMLATSS.G.Q.
Retrocopy SGICSAKDLKMARSLVPKALEPYVTKMANGTFGDMFTMSGSTSNDMQLSASDLTNTVDGMLATSSSGIQC

Parental  SGSRVETPVSYVGEDDEDDDDFNENDEDD
          SG.RVETPV....EDD....DFN..D..D
Retrocopy SGFRVETPVVEEEEDDSKNNDFNDDDKYD

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	13.02 RPM
SRP051959_heart	0.00 RPM	9.00 RPM
SRP051959_kidney	0.00 RPM	11.47 RPM
SRP051959_liver	0.00 RPM	19.73 RPM
SRP051959_lung	0.02 RPM	12.27 RPM
SRP051959_lymph_node	0.00 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_179 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_179 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_61

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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,