RetrogeneDB ID: retro_ptro_716

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:100877433..100878883(+)
• Located in intron of: ENSPTRG00000005346

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGA
• Ensembl ID: ENSPTRG00000021684
• Aliases: None
• Description: None

Sequence

>retro_ptro_716
ATGGCGTATAAAGGAGAAGGTGGGCATGGCCAGCCTCCCTCAGCTACACTGTCTCAGGTTAGCCCTGGAAGTCTTTACAC
ACGTAGAACCCATACCCATTATATATGTATGGCATCTGACTTTTTCTACCCAAATATGGGAGGTGTGGAAAGCCACATTT
ACCAGCTCCCTCAGTGCCTGATTGGAAGAGGGGATAAGGTTATAATTGTCATCCATGCTTATGGAAATCGAAAAGGCATC
CGTTACCTCACTAATGACCTCAAAGTCTATTACGTGCCTCTGAAAGTCATGTATAACCAGTCTATGGCCATGACCCTCTT
TCACAGTCTGCCATTGCTCAAGTACATATTTGTTCAGGAGAGAGTCACAATAATCCATTCACATAGTTCATTTTCTGCCA
TGGCCCATGATGTTCTCTTCCATGCCAAGACAATGGGGCTTCAAACAGTCTTAACAGACCATCCCCTTTCTGGATTTGCT
AAGGTCCATTCAGTGCTTACAAACAAACTTCTAACTGTGTCTCTTTGTGACACAAGCCGTATCATTTGCGTTTCTTATAC
TAGTAAGGAAAATACCGTACTACGAGCAGCACTGATTACTGAAATAGTGTCTGTCATTCCTAACGCTGTAGATCCTACTG
ACTTCACTCCAGACCCATTTAGAAGGCATGATAGTATAACTATTGTTGTCAGCAGACTTGTTTACAGAAAGGGAACCAGT
TTGGTTAGTGGTATTATACCCAAACTCTTGTCAGAAATATTCAGATTTAAATTTCATAATTGGAGGAGAGGGACCAAAGA
GAATCATTTTGCAAGAAGTTCCGGAAAGATACCAGTTGCATGACAGGGTGCATCTTTTGGGAGCTTTAGAACACAAGAAT
GTTAGAAATGTCTTAGTTCAAGGACATATTTTTCTTAATACCTCCCTTACTGAAGCATTCTGCATGGCGATCATGGAAGC
AGCCAGCTGTGGTTTACAGGTTGTAAGTACCAGGGTTGGTGGAATTCCTGAGGTGCTTCCAGAAAATCTTACTATTTTAT
GAGAAACTTCAGTAAAATCTTTGTGTGAGGGATTGGAAAAAGCTATTTTCCAACTGAAGTCAGGGGCATTGCTGGCTCCA
GAAAATATCCGTAACATAGTAAAGACTTTCCACACCTGAAGGAATGTTGTGGAGAGAACTGAAAAAGTATATGACCAAGT
ATCAGTGGAATCTGTGTTGCCAATGGACAAACAACTGGACAGACTTATTTCTCACAGTGGACCAGTAACAGGCTACATCT
TTGCTTTGTTGGCTGTTTTCAACTTCCTCTTCCTCATTTTCTTGAGATGGATGGCTCCAGATTCTATCATTGATACTGGA
ATAGATGCCACTGGGCCAAGGGGTGCCTGGACTCATAAATGTTCTCACAGTAAAAGAGGGGGTGAGAATATTAAGATATC
TAAAACCAGG

Alignment

ORF - retro_ptro_716 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.19 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MACRGGAGNGHRASATLSRVSPGSLYTCRTRTHNICMVSDFFYPNMGGVESHIYQLSQCLIERGHKVIIV
          MA..G..G.G...SATLS.VSPGSLYT.RT.TH.ICM.SDFFYPNMGGVESHIYQL.QCLI.RG.KVIIV
Retrocopy MAYKGEGGHGQPPSATLSQVSPGSLYTRRTHTHYICMASDFFYPNMGGVESHIYQLPQCLIGRGDKVIIV

Parental  THAYGNRKGIRYLTNGLKVYYLPLKVMYNQSTATTLFHSLPLLRYIFVRERVTIIHSHSSFSAMAHDALF
          .HAYGNRKGIRYLTN.LKVYY.PLKVMYNQS.A.TLFHSLPLL.YIFV.ERVTIIHSHSSFSAMAHD.LF
Retrocopy IHAYGNRKGIRYLTNDLKVYYVPLKVMYNQSMAMTLFHSLPLLKYIFVQERVTIIHSHSSFSAMAHDVLF

Parental  HAKTMGLQTVFTDHSLFGFADVSSVLTNKLLTVSLCDTNHIICVSYTSKENTVLRAALNPEIVSVIPNAV
          HAKTMGLQTV.TDH.L.GFA.V.SVLTNKLLTVSLCDT..IICVSYTSKENTVLRAAL..EIVSVIPNAV
Retrocopy HAKTMGLQTVLTDHPLSGFAKVHSVLTNKLLTVSLCDTSRIICVSYTSKENTVLRAALITEIVSVIPNAV

Parental  DPTDFTPDPFRRHDSITIVVVSRLVYRKGIDLLSGIIPEL-CQKYPDLNFIIGGEGPKRIILEEVRERYQ
          DPTDFTPDPFRRHDSITIVV.SRLVYRKG..L.SGIIP.L.CQKY.DLNFIIGGEGPKRIIL.EV.ERYQ
Retrocopy DPTDFTPDPFRRHDSITIVV-SRLVYRKGTSLVSGIIPKL>CQKYSDLNFIIGGEGPKRIILQEVPERYQ

Parental  LHDRVRLLGALEHKDVRNVLVQGHIFLNTSLTEAFCMAIVEAASCGLQVVSTRVGGIPEVLPENLIILCE
          LHDRV.LLGALEHK.VRNVLVQGHIFLNTSLTEAFCMAI.EAASCGLQVVSTRVGGIPEVLPENL.IL.E
Retrocopy LHDRVHLLGALEHKNVRNVLVQGHIFLNTSLTEAFCMAIMEAASCGLQVVSTRVGGIPEVLPENLTIL*E

Parental  PSVKSLCEGLEKAIFQLKSGTLPAPENIHNIVKTFYTWRNVAERTEKVYDRVSVEAVLPMDKRLDRLISH
          .SVKSLCEGLEKAIFQLKSG.L.APENI.NIVKTF.T.RNV.ERTEKVYD.VSVE.VLPMDK.LDRLISH
Retrocopy TSVKSLCEGLEKAIFQLKSGALLAPENIRNIVKTFHT*RNVVERTEKVYDQVSVESVLPMDKQLDRLISH

Parental  CGPVTGYIFALLAVFNFLFLIFLRWMTPDSIIDVAIDATGPRGAWTNNYSHSKRGGENNEISETR
          .GPVTGYIFALLAVFNFLFLIFLRWM.PDSIID..IDATGPRGAWT...SHSKRGGEN..IS.TR
Retrocopy SGPVTGYIFALLAVFNFLFLIFLRWMAPDSIIDTGIDATGPRGAWTHKCSHSKRGGENIKISKTR

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	4.43 RPM
SRP007412_cerebellum	0.00 RPM	6.99 RPM
SRP007412_heart	0.00 RPM	2.68 RPM
SRP007412_kidney	0.03 RPM	7.01 RPM
SRP007412_liver	0.00 RPM	5.60 RPM
SRP007412_testis	0.00 RPM	7.38 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_716 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_716 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_716 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1050
Gorilla gorilla	retro_ggor_828
Pongo abelii	retro_pabe_876

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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,