RetrogeneDB ID: retro_cjac_4146

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:28717570..28718111(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGF
• Ensembl ID: ENSCJAG00000000680
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class F [Source:HGNC Symbol;Acc:8962]

Sequence

>retro_cjac_4146
ATGAAAGACACTGATATCAAGAGACTATTGTATAATCATTTTTATGCATATTTTCAATTAGCCTAATCATCTTCATTCCA
TCATTCTTTTCAGAGAACTTCTCAGTATTGGAAACACACTTAATATGGTTATACATCTGCTGTGATTTTCTAAGTGCTGT
CAATCCTGTATTATATTTAGTAGCAAAACCAAATGCATCCTCTAAAAGAAGTTTATCATCACCCAAGGTGACCAGATTTT
TGGAATGATGTATCTAATTTCTTATGTCTTGTTTCATGAAATTCATGTAATTTTTGTTCTATATGGAGCACCACCATTAG
AGTTGAAGACGGAAATATTTTTATTTGTGGTTATTTTGCCTGCTTTTACTACTCTACCAAGTTTATTTTGCTTAGGACCA
AATCTCAAAGCATGGATAAGAGTTTTCACTGAAAAGGGAGTTATATTCACTTGGGAGAGTGTCCATATCACTACAATTTA
TAGTTTTTTTGGAACATATCTTGGAGCACTTTGTATACCACAGGATTGGAAAAGACCATGG

Alignment

ORF - retro_cjac_4146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.22 %
• Parental protein coverage: 82.65 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKDTDIKRLLYTHL-LCIFSIILSVFIPSLCLENFSLLETHLTWLCTCSGFVTAVNLVLYLVVKPNASSK
          MKDTDIKRLLY.H..LCIFSI.L..FIPS...ENFS.LETHL.WL..C..F..AVN.VLYLV.KPNASSK
Retrocopy MKDTDIKRLLYNHF<LCIFSISLIIFIPSFFSENFSVLETHLIWLYICCDFLSAVNPVLYLVAKPNASSK

Parental  RSSLSHKVTRFLK-CCIYFLMSCFSF-HVIFVLYGAPLIELALETFLFAVILSTFTTVPCLCLLGPNLKA
          RS..S.KVTRFL..C..........F.HVIFVLYGAP..EL..E.FLF.VIL..FTT.P.L..LGPNLKA
Retrocopy RSLSSPKVTRFLE*CI*FLMSCFMKF<HVIFVLYGAPPLELKTEIFLFVVILPAFTTLPSLFCLGPNLKA

Parental  WLRVFSRNGVTSIWENSLQITTISSFVGAWLGALPIPLDWERPW
          W.RVF...GV...WE.S..ITTI.SF.G..LGAL.IP.DW.RPW
Retrocopy WIRVFTEKGVIFTWE-SVHITTIYSFFGTYLGALCIPQDWKRPW

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	3.22 RPM
SRP051959_heart	0.00 RPM	3.24 RPM
SRP051959_kidney	0.00 RPM	5.08 RPM
SRP051959_liver	0.00 RPM	2.49 RPM
SRP051959_lung	0.00 RPM	3.40 RPM
SRP051959_lymph_node	0.00 RPM	2.26 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.75 RPM
SRP051959_spleen	0.00 RPM	2.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4146 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4146 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4146 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4801
Pan troglodytes	retro_ptro_3192
Gorilla gorilla	retro_ggor_2988
Pongo abelii	retro_pabe_3733
Macaca mulatta	retro_mmul_2559

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028483	1 retrocopy	retro_acar_103,
Callithrix jacchus	ENSCJAG00000000680	2 retrocopies	retro_cjac_4146 , retro_cjac_481,
Dasypus novemcinctus	ENSDNOG00000007278	2 retrocopies	retro_dnov_1980, retro_dnov_502,
Dasypus novemcinctus	ENSDNOG00000025474	1 retrocopy	retro_dnov_602,
Dipodomys ordii	ENSDORG00000006083	1 retrocopy	retro_dord_234,
Homo sapiens	ENSG00000151665	3 retrocopies	retro_hsap_3277, retro_hsap_4217, retro_hsap_4801,
Gorilla gorilla	ENSGGOG00000024478	3 retrocopies	retro_ggor_2229, retro_ggor_2825, retro_ggor_2988,
Myotis lucifugus	ENSMLUG00000008686	1 retrocopy	retro_mluc_1471,
Macaca mulatta	ENSMMUG00000005389	2 retrocopies	retro_mmul_1173, retro_mmul_2559,
Monodelphis domestica	ENSMODG00000000968	1 retrocopy	retro_mdom_1771,
Mustela putorius furo	ENSMPUG00000012037	1 retrocopy	retro_mputfur_810,
Nomascus leucogenys	ENSNLEG00000016924	3 retrocopies	retro_nleu_1115, retro_nleu_1455, retro_nleu_2882,
Oryctolagus cuniculus	ENSOCUG00000001130	1 retrocopy	retro_ocun_618,
Otolemur garnettii	ENSOGAG00000026734	1 retrocopy	retro_ogar_1699,
Pongo abelii	ENSPPYG00000012438	3 retrocopies	retro_pabe_2710, retro_pabe_3450, retro_pabe_3733,
Pan troglodytes	ENSPTRG00000011895	2 retrocopies	retro_ptro_2863, retro_ptro_3192,
Ictidomys tridecemlineatus	ENSSTOG00000001373	1 retrocopy	retro_itri_989,
Tupaia belangeri	ENSTBEG00000000891	1 retrocopy	retro_tbel_3809,
Tarsius syrichta	ENSTSYG00000002842	3 retrocopies	retro_tsyr_1497, retro_tsyr_1556, retro_tsyr_1820,
Vicugna pacos	ENSVPAG00000000314	1 retrocopy	retro_vpac_478,