RetrogeneDB ID: retro_pabe_3733

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:30247141..30247760(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGF
• Ensembl ID: ENSPPYG00000012438
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class F [Source:HGNC Symbol;Acc:8962]

Sequence

>retro_pabe_3733
ATGAAAGACACTGATATCAAGAGAGTATTGTATAATCATCTTTTTGCATGTTTTCAATTAGCTTGATCATCTTCATTCCA
TCATTCTTTTTGGAGAACTTCTCAATATTGGAAGCACACTTAATATGGTTGTGCATCTGTTGTGTTTTTCTAACTGCTGT
CAATCCAGTATTATATTTAGTAGTGAAACCAAATGCATCCTCTAAAAGAAGTTTATCATCACACAAGGTGACCAGATTTT
TGGAATGCTGTATTAATTTCTTATGTCTTGTTTCTTGCATGTAATTCATGTAATTTTTGTTCTATACGGAGTGCCACCAT
TAGAGTTGAAGATGGAAACATTTTTATTTGTGGTTATTTTGTCTGCTTTTACTACTGTACCAAGTTTATTTTTGTTAGGA
CCAAATCTCAAAGCATGGATAAGAGTTTTCACTGGAAAGGGAGTTATATTCACTTGGGAGAATAGTGTCCAGATCACTAC
AATTTCTAGTTTTGTGGGAACATGTCTTGGAGTACTTTCTATACCACTGGATTGGAAAAGACCGTGGCAGATAAGGAAAC
TAACACCTAGATGATATGTAACATTCTCGATGTCAGTGAGCTCGTACATATGGCCCATC

Alignment

ORF - retro_pabe_3733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.9 %
• Parental protein coverage: 93.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKDTDIKRLLYTHLL-CIFSIILSVFIPSLFLENFSILETHLTWLCICSGFVTAVNLVLYLVVKPNTSSK
          MKDTDIKR.LY.HL..C.FSI.L..FIPS.FLENFSILE.HL.WLCIC..F.TAVN.VLYLVVKPN.SSK
Retrocopy MKDTDIKRVLYNHLF<CMFSISLIIFIPSFFLENFSILEAHLIWLCICCVFLTAVNPVLYLVVKPNASSK

Parental  RSSLSHKVTRFLKCCIYFL-MSCFS--FHVIFVLYGAPLIELALETFLFAVILSAFTTVPCLCLLGPNLK
          RS..SHKVTRFL.CCI.FL.MSCF....HVIFVLYG.P..EL..ETFLF.VILSAFTTVP.L.LLGPNLK
Retrocopy RSLSSHKVTRFLECCINFL<MSCFLHVIHVIFVLYGVPPLELKMETFLFVVILSAFTTVPSLFLLGPNLK

Parental  AWLRVFSRNGVTSIWENSLQITTISSFVGAWLGALPIPLDWERPWQVWPISCTLGATFGYVAGLVISPL
          AW.RVF...GV...WENS.QITTISSFVG..LG.L.IPLDW.RPWQ..........TF.......I.P.
Retrocopy AWIRVFTGKGVIFTWENSVQITTISSFVGTCLGVLSIPLDWKRPWQIRKLTPR*YVTFSMSVSSYIWPI

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
SRP007412_brain_prefrontal_cortex	0.00 RPM	6.08 RPM
SRP007412_cerebellum	0.00 RPM	7.17 RPM
SRP007412_heart	0.00 RPM	26.31 RPM
SRP007412_kidney	0.00 RPM	10.44 RPM
SRP007412_liver	0.00 RPM	8.02 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3733 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3733 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3733 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
Macaca mulatta	retro_mmul_2559
Callithrix jacchus	retro_cjac_4146

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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,