RetrogeneDB ID: retro_cjac_3175

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:3245778..3246281(+)
• Located in intron of: ENSCJAG00000007208

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDFIP1
• Ensembl ID: ENSCJAG00000018271
• Aliases: None
• Description: Nedd4 family interacting protein 1 [Source:HGNC Symbol;Acc:17592]

Sequence

>retro_cjac_3175
TTGGCATCGGTGGCATCAGCACCAGCTGAGCTGGTCTGCAGCAGTGGGTACCAACATTTATAGAATGAGGAAGAGCCTGA
AGAACCCAAGAAGGCTTCCGGTGAGGTTCCTCCATCTTAACAGCAGCAACTCTGCCCAGAGTATGGTACGTTTGAGTACG
AAGATGAGTCTGATTTTCTAATGCCCCTGTTTTACAATGTGGTTACAAACATTACCAATTTATAATTAAGTCATGAGAAT
CGAGGCTGACACTATTTCTTTGGTTCCTGGAAGAGATGAAGATTTTGTGAGACAAGATGATTTTGATGATGCTGACCAGC
TGAGGACAGGAATTTTTTTGGTTAACTTTTTTTCCTGGCCTTCCTCTTAACTGGATGGAGTTTTCTCCTGTCTTCTTTCC
TAACTGCTCAGTGGCAGGAAGATATGACACCATTTCAGAATTTGGTCTCTTTCTGTTTAAGTGGGTCCTGAGAGGCAGAT
TTCTAACCTGTTTCCCTTGATAC

Alignment

ORF - retro_cjac_3175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.02 %
• Parental protein coverage: 77.38 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LALAALAAVEPACGSRYQQLQNEEESGEPEQAAGDAPPPYSSISAESAAYFDYKDESGFPKPPSYNVAT-
          LA..A.A..E..C.S.YQ.L.NEEE..EP..A.G..PP............F.Y.DES.F..P..YNV.T.
Retrocopy LASVASAPAELVCSSGYQHL*NEEEPEEPKKASGEVPPS*QQQLCPEYGTFEYEDESDFLMPLFYNVVT>

Parental  TLPSYDEAERTKAEATIPLVPGRDEDFVGRDDFDDADQLRIGNDGIFM-LTFFMAFLFNWIGFFLSFCLT
          TLP.Y....R..A..TI.LVPGRDEDFV..DDFDDADQLR.G...IF..LTFF.....NW..F...F...
Retrocopy TLPIYN*VMRIEAD-TISLVPGRDEDFVRQDDFDDADQLRTG---IFL>LTFFPGLPLNWMEFSPVFFPN

Parental  TSAAGRYGAISGFGLSLIKWILIVRFSTYFPGY
          .S.AGRY..IS.FGL.L.KW.L..RF.T.FP.Y
Retrocopy CSVAGRYDTISEFGLFLFKWVLRGRFLTCFP*Y

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	0.13 RPM	46.95 RPM
SRP051959_heart	0.00 RPM	43.17 RPM
SRP051959_kidney	0.11 RPM	100.06 RPM
SRP051959_liver	0.89 RPM	77.22 RPM
SRP051959_lung	0.15 RPM	48.40 RPM
SRP051959_lymph_node	0.00 RPM	42.42 RPM
SRP051959_skeletal_muscle	0.00 RPM	33.63 RPM
SRP051959_spleen	0.00 RPM	49.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3175 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3175 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3175 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1091
Pan troglodytes	retro_ptro_743
Gorilla gorilla	retro_ggor_859
Pongo abelii	retro_pabe_908
Macaca mulatta	retro_mmul_846

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000047747	1 retrocopy	retro_btau_766,
Callithrix jacchus	ENSCJAG00000018271	1 retrocopy	retro_cjac_3175 ,
Callithrix jacchus	ENSCJAG00000021282	2 retrocopies	retro_cjac_2643, retro_cjac_2644,
Equus caballus	ENSECAG00000021907	1 retrocopy	retro_ecab_261,
Homo sapiens	ENSG00000131507	1 retrocopy	retro_hsap_1091,
Gorilla gorilla	ENSGGOG00000004879	1 retrocopy	retro_ggor_859,
Macaca mulatta	ENSMMUG00000016787	1 retrocopy	retro_mmul_846,
Pongo abelii	ENSPPYG00000015896	1 retrocopy	retro_pabe_908,
Pan troglodytes	ENSPTRG00000017358	1 retrocopy	retro_ptro_743,
Sarcophilus harrisii	ENSSHAG00000002466	1 retrocopy	retro_shar_738,
Sus scrofa	ENSSSCG00000025295	1 retrocopy	retro_sscr_301,
Ictidomys tridecemlineatus	ENSSTOG00000005153	1 retrocopy	retro_itri_1454,