RetrogeneDB ID: retro_pabe_876

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:101886625..101888089(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGA
• Ensembl ID: ENSPPYG00000020142
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class A [Source:HGNC Symbol;Acc:8957]

Sequence

>retro_pabe_876
ATGGCGTATAAAGGAGAAGGTGGGCATGGCCAGCCTCCCTCAGCTACACTCTCTCAGGTTAGCCCTGGAAGTCTTTACAC
ACGTAGAACCCGTACCCATAATATATGTATGGCATCTGACTTTTTCTACCCAAATATGGGAGGTGTGGAAAGCCACATTT
ACCAGCTCCCTCAGTGCCCTGATTGGAAGACGGCATAAGGTTATAATTGTCATTCATGCTTACGGAAATCGAAAAGGCAT
CCGTTACCTCACTAATGACCTCAAAGTCTATTACTTGCCTCTGAAAGTCATGTATAACCCAGTCTATGGCCATGACCCTC
TTTCACAGTCTGCCATTGCTCAAGGTACATATTTTGTTCCAGGAGAGAATCACAATAATCCATTCACATAGTTCATTTTC
TGCCATGGCCCATGATGTTCTCTTCCATGCCAAGACAATGGGGCTTCAAACAGTCTTAACAGACCATTCCCTTTCTGGAT
TTGCTAAGGTCCACTCGGTGCTTACAAACAAACTTCTAACTGTGTCTCTTTGTGACACAAGCCGTATCATTTGTGTTTCT
ATATACTAGTAAGGAAAATACCGTAGTACGAGCGAGCACTGACTACTGAAATAGTGTCTGTCATTCCTAATGCTGTAGAT
CCTACTGACTTCACTCCAGACCCATTTAGCAAGGCATGATAGTGTAACTATTGTTGTCAGCAGACTTGTTTACAGAAAGG
GAACCAATTTGCTTAGTGGTATTATACCCAAACTCTTGTCAGAAATATTCAGATTTAAATTTCATAATTGGAGGAGAGGG
ACCAAAGAGAATCATTTTGCAAGAAGTTCCGGAAAGATACCAGTTGCACGACAGGGTGCATCTTTTGGGAGCTTTAGAAC
ACAAGAATGTTAGAAACTGTCTTAGTTCAAGGACATATTTTTCTTAATACCTCCCTTACTGAAGCATTCTGCGTGGCGAT
TGTGGAAGAAGCCAGCTGTAGTTTACAGGTTGTAAGTACCAGAGTTGGTGGGATTCCTGAGGTGCTTCCAGAAAATCTTA
TTATTTTATGAGAAACTTCAGTAAAATCTTTGTGTGAGGGATTGGAAAAAGCTATTTTCCAACTGAAGTCAGGGGGCATT
GCTGGCTCCAGAAAATATCCATAACATAGTAAAGACTTTCTACACCTGAAGGAATGTTGTGGAGAGAACTGAAAAAGTGT
ATGACCAAGTATCAGTGGAATCTGTGTTGTCAATGGACAAACAAGCTGGACAGAACTTGTTTCTCACTTTGGACCAGTAA
CAGGCTACATCTTTGCTTTGTTGGGGTGTTTTCAATTTCCTCGTCCTCATTTTCTGGAAGATGGATGACTCCAGATTCTA
TCATTGATACTGGAATAGATGCCACTGGGCCAAGGGGTGCCTGGACTCATAAATGTTCTCACAGTAAAAGAGGGGGTGAG
AATATTAAGATATCTAAAACCAGG

Alignment

ORF - retro_pabe_876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 12

Retrocopy - Parental Gene Alignment:

Parental  MARRGGAGDGHRASATLSRVSPGSLYTCRTHTHNICMVSDFFYPNMGGVESHIYQLSQC-LIERGHKVII
          MA..G..G.G...SATLS.VSPGSLYT.RT.THNICM.SDFFYPNMGGVESHIYQL.QC.LI.R.HKVII
Retrocopy MAYKGEGGHGQPPSATLSQVSPGSLYTRRTRTHNICMASDFFYPNMGGVESHIYQLPQC>LIGRRHKVII

Parental  VTHAYGNRKGIRYLTNGLKVYYLPLKVMYN-QSTATTLFHSLPLLR-YIFVRERVTIIHSHSSFSAMAHD
          V.HAYGNRKGIRYLTN.LKVYYLPLKVMYN.QS.A.TLFHSLPLL...I...ER.TIIHSHSSFSAMAHD
Retrocopy VIHAYGNRKGIRYLTNDLKVYYLPLKVMYN>QSMAMTLFHSLPLLKVHILFQERITIIHSHSSFSAMAHD

Parental  ALFHAKTMGLQTVFTDHSLFGFADVSSVLTNKLLTVSLCDTNHIICVS-YTSKENTVLRA-ALNPEIVSV
          .LFHAKTMGLQTV.TDHSL.GFA.V.SVLTNKLLTVSLCDT..IICVS.YTSKENTV.RA.AL..EIVSV
Retrocopy VLFHAKTMGLQTVLTDHSLSGFAKVHSVLTNKLLTVSLCDTSRIICVS>YTSKENTVVRA>ALTTEIVSV

Parental  IPNAVDPTDFTPDPFR-RHDSITIVVVSRLVYRKGIDLLSGIIPEL-CQKYPDLNFIIGGEGPKRIVLEE
          IPNAVDPTDFTPDPF..RHDS.TIVV.SRLVYRKG..LLSGIIP.L.CQKY.DLNFIIGGEGPKRI.L.E
Retrocopy IPNAVDPTDFTPDPFS>RHDSVTIVV-SRLVYRKGTNLLSGIIPKL>CQKYSDLNFIIGGEGPKRIILQE

Parental  VRERYQLHDRVRLLGALEHKDVRN-VLVQGHIFLNTSLTEAFCMAIVEAASCGLQVVSTRVGGIPEVLPE
          V.ERYQLHDRV.LLGALEHK.VRN.VLVQGHIFLNTSLTEAFC.AIVE.ASC.LQVVSTRVGGIPEVLPE
Retrocopy VPERYQLHDRVHLLGALEHKNVRN>VLVQGHIFLNTSLTEAFCVAIVEEASCSLQVVSTRVGGIPEVLPE

Parental  NLIILCEPSVKSLCEGLERAIFQLKS-GTLPAPENIHNIVKTFYTWRNVAERTEKVYDRVSVEAVLPMDK
          NLIIL.E.SVKSLCEGLE.AIFQLKS.G.L.APENIHNIVKTFYT.RNV.ERTEKVYD.VSVE.VL.MDK
Retrocopy NLIIL*ETSVKSLCEGLEKAIFQLKS>GALLAPENIHNIVKTFYT*RNVVERTEKVYDQVSVESVLSMDK

Parental  -RLDR-LISHCGPVTGYIFALL-AVFNFLFLIFL-RWMTPDSIIDVAVDATGPRSAWTNNCSHSKRGSEN
          ..LDR.L.SH.GPVTGYIFALL..VFNFL.LIF..RWMTPDSIID...DATGPR.AWT..CSHSKRG.EN
Retrocopy >KLDR>LVSHFGPVTGYIFALL>GVFNFLVLIFW>RWMTPDSIIDTGIDATGPRGAWTHKCSHSKRGGEN

Parental  NEISETR
          ..IS.TR
Retrocopy IKISKTR

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	3.04 RPM
SRP007412_cerebellum	0.12 RPM	9.61 RPM
SRP007412_heart	0.00 RPM	2.20 RPM
SRP007412_kidney	0.03 RPM	5.83 RPM
SRP007412_liver	0.03 RPM	3.76 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_876 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_876 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_876 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1050
Pan troglodytes	retro_ptro_716
Gorilla gorilla	retro_ggor_828

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006415	1 retrocopy	retro_chof_2311,
Homo sapiens	ENSG00000165195	1 retrocopy	retro_hsap_1050,
Gorilla gorilla	ENSGGOG00000007293	1 retrocopy	retro_ggor_828,
Nomascus leucogenys	ENSNLEG00000009352	1 retrocopy	retro_nleu_2070,
Ochotona princeps	ENSOPRG00000015381	1 retrocopy	retro_opri_1065,
Pongo abelii	ENSPPYG00000020142	1 retrocopy	retro_pabe_876 ,
Pan troglodytes	ENSPTRG00000021684	1 retrocopy	retro_ptro_716,
Rattus norvegicus	ENSRNOG00000003554	1 retrocopy	retro_rnor_2566,