RetrogeneDB ID: retro_ptro_2863

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:122902444..122903092(+)
• Located in intron of: ENSPTRG00000021349

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGF
• Ensembl ID: ENSPTRG00000011895
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class F [Source:HGNC Symbol;Acc:8962]

Sequence

>retro_ptro_2863
ATGAAAGATACTGACATCAAAAAATTACTTTATACCCATATTTTATGCATATTTTCAATTATCCTAAGTGTCTTCATTCC
ATCATTCTTCTTGGAGAACTTCTCAATATTGTAAACACACTTGACATGGTTGTGCATATGTTCTGGTTTTGTAGCTGCTG
TCAATCTAGTATTATATTTAGTAGTGAAACCAAATGCATCCCCTAAAAAAGTTCATTATCACACAAGGTAACTTGATTTT
TGAAATGCTGTGTCTACCTTCTTTTGTCCTGTTTCTCCTTCCATGTAATTTTTGTTCTATATGGAGCTAATAGAGTTGGT
GTTGGAAACATTTTTATTTGCAGTCATTTTGTCTACTTTTACCACTGTACCTTATGTTTGTTAGAACCAAATCTCAAAAG
CATAGCTTAGAGTTTTCAGTAGAAATGGAGTTACAGCCATTTGGGAGAATAGTCTCCAGATCATTACAATTTCTAGTTTT
GTAGGAGCATAACTTGAAGCACTGCCAATACCACTGAGTGGAGAAAGACCATGGCAGGTATGGCCCATCTCCTATATGCT
TGGAGTGACCTTTAGCAACATGGATGGACTTGTTATTTTACCATTCTGGATATACTGGAATATAAAGCAATTTCTATACA
AGAACAAT

Alignment

ORF - retro_ptro_2863 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKDNDIKRLLYTHLLCIFSIILSVFIPSLFLENFSILETHLTWLCICSGFVTAVNLVLYLVVKPNTSSK-
          MKD.DIK.LLYTH.LCIFSIILSVFIPS.FLENFSIL.THLTWLCICSGFV.AVNLVLYLVVKPN.S.K.
Retrocopy MKDTDIKKLLYTHILCIFSIILSVFIPSFFLENFSIL*THLTWLCICSGFVAAVNLVLYLVVKPNASPK<

Parental  RSSLSHKVTRFLKCCIYFLMSCFSFHVIFVLYGAPLIELALETFLFAVILSTFTTVPCLCLLGPNL-KAW
          .SSLSHKVT.FLKCC.Y.L.SCFSFHVIFVLYGA.........F.............CL..L.PNL.KA.
Retrocopy KSSLSHKVT*FLKCCVYLLLSCFSFHVIFVLYGANRVGVG-NIFICSHFVYFYHCTLCL--LEPNL>KA*

Parental  LRVFSRNGVTSIWENSLQITTISSFVGAWLGALPIPLDWERPWQVWPISCTLGATFGYVAGLVISPLWIY
          LRVFSRNGVT.IWENSLQI.TISSFVGA.L.ALPIPL..ERPWQVWPIS..LG.TF....GLVI.P.WIY
Retrocopy LRVFSRNGVTAIWENSLQIITISSFVGA*LEALPIPLSGERPWQVWPISYMLGVTFSNMDGLVILPFWIY

Parental  WNRKQLTYKNN
          WN.KQ..YKNN
Retrocopy WNIKQFLYKNN

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	0.04 RPM	5.52 RPM
SRP007412_cerebellum	0.00 RPM	1.72 RPM
SRP007412_heart	0.00 RPM	13.12 RPM
SRP007412_kidney	0.00 RPM	6.46 RPM
SRP007412_liver	0.00 RPM	2.39 RPM
SRP007412_testis	0.11 RPM	5.06 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2863 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2863 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2863 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4217
Gorilla gorilla	retro_ggor_2825
Pongo abelii	retro_pabe_3450

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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,