RetrogeneDB ID: retro_cjac_481

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:167648480..167649132(+)
• Located in intron of: ENSCJAG00000006461

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_481
ATGAAAGACACTGGCATTAAAAAACTACCTTATCCATGTTTTACACATATTTTCAATTGTCCTAAGTGTCTTCATTCTAT
CATTCTTCTTGGAGAACTTCTCAGTATTGTAAACATACTTGACACGGTTGTACAAACCCCACGGTTGTTCTGGGTTTGTA
GCTGCTATCAATCTAGTATCATATTTAGTATGAAACCAAATGCATCCTTTAAAAAGTTCATTATCACACAAGGTAACTTG
ATTTTTTAAATCCTGTAACTACACTCTTTTGTCCTGTTTCTTTTCTCATGGAATTTTTGTTTTATATTAAGCTAATAGAG
TTGGTGTTGGAAACATTTTTATTTGCAGTCATTTTGTCTACTTTTACCACTGTGCCTTATGTTTGTTAGGACCAAATCTC
AAAGCATGGCTTAGAGTTCTCAGCAGAAATGGAATTGCAGCCATTTGGGAAAATAGTCTCCAGATCATTACAGTTTGTAG
TTTTGTAGAAGCATAGCTTGAAGCACTGCCAATATGACTGAGTAGGAAAAGACCATGGCAGGTATGGCCCATCTCCTATA
TGCTTGGAGTAAGCTTCAGCCACATGGTTGGCCTTGTTATTTCACCATTCTGGATATACTGGAATATAAAGCAATTTCTA
TACAAGAACAAT

Alignment

ORF - retro_cjac_481 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.85 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKDTD-IKRLLYTHLLCIFSIILSVFIPSLCLENFSLLETHLTWLCT---CSGFVTAVNLVLYLVVKPNA
          MKDT...K..L..H.L.IFSI.LSVFI.S..LENFS.L.T.LT.L.....CSGFV.A.NLV.YL.V....
Retrocopy MKDTG>LKNYLI-HVLHIFSIVLSVFILSFFLENFSVL*TYLTRLYKPHGCSGFVAAINLVSYL-V*NQM

Parental  SSKRSSLSHKVTRFLKCCIYFLMSCFSFHVIFVLYGAPLIELALETFLFAVILSTFTTVPCLCLLGPNLK
          ....SSLSHKVT.F.K.C.Y.L.SCF..H.IFVLY.A.........F.............CL..LGPNLK
Retrocopy HPLKSSLSHKVT*FFKSCNYTLLSCFFSHGIFVLY*ANRVGVG-NIFICSHFVYFYHCALCL--LGPNLK

Parental  AWLRVFSRNGVTSIWENSLQITTISSFVGAWLGALPIPLDWERPWQVWPISCTLGATFGYVAGLVISPLW
          AWLRV.SRNG...IWENSLQI.T..SFV.A.L.ALPI.L...RPWQVWPIS..LG..F....GLVISP.W
Retrocopy AWLRVLSRNGIAAIWENSLQIITVCSFVEA*LEALPI*LSRKRPWQVWPISYMLGVSFSHMVGLVISPFW

Parental  IYWNRKQLTYKNN
          IYWN.KQ..YKNN
Retrocopy IYWNIKQFLYKNN

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	0.53 RPM	3.22 RPM
SRP051959_heart	0.46 RPM	3.24 RPM
SRP051959_kidney	0.49 RPM	5.08 RPM
SRP051959_liver	0.30 RPM	2.49 RPM
SRP051959_lung	0.37 RPM	3.40 RPM
SRP051959_lymph_node	0.46 RPM	2.26 RPM
SRP051959_skeletal_muscle	0.57 RPM	2.75 RPM
SRP051959_spleen	0.88 RPM	2.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_481 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_481 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_481 has 0 orthologous retrocopies within eutheria group .

---

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,