RetrogeneDB ID: retro_ggor_828

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 12:99839291..99840741(+)
• Located in intron of: ENSGGOG00000003196

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGA
• Ensembl ID: ENSGGOG00000007293
• Aliases: None
• Description: None

Sequence

>retro_ggor_828
ATGGCGTATAAAGGAGAAGGTGGGCATGGCCAGCCTCCCTCAGCTACACTGTCTAAGGTTAGCCCTGGAAGTCTTTACAC
ACGTAGAACCCATACCCGTAATATATGTATGGCATCTGACTTTTTCTACCCAAATATGGGAGGTGTGGAAAGCCACATTT
ACCAGCTCCCTCAGTGCCTGATTGGAAGAGGGGATAAGGTTATAATTGTCATCCATGCTTATGGAAATCGAAAAGGCATC
CGTTACCTCACTAATGACCTCAAAGTCTATTTCTTGCCTCTGAAAGTCATGTATAACCAGTCTATGGCCATGACCCTCTT
TCACAGTCTGCCATTGCTCAAGTGCATATTTGTTCAGGAGAGAGTCACAATAATCCATTCACATAGTTCATTTTCTGCCA
TGGCCTATGATGTTCTCTTCCATGCCAAGACAATGGGGCTTCAAACAGTCTTAACAGACCATCCCCTTTCTGGATTTGCT
AAGGTCCATTCAGTGCTTACAAACAAACTTCTAACTGTGTCTCTTTGTGACGCAAGCCGTATCATTTGCGTTTCTTATAC
TAGTAAGGAAAATACCGTACTACGAGCAGCACTGATTACTGAAATAGTGTCTGTCATTCCTAACGCTGTAGATCCTACTG
ACTTCACTCCAGACCCATTTAGAAGGCATGATAGTATAACTATTGTTGTCAGCAGACTTGTTTACAGAAAAGGAACCAAT
TTGGTTAGTGGTATTATACCCAAACTCTTGTCAGAAATATTCAGATTTAAATTTCATCATTGGAGGAGAGGGACCAAACA
GAATCATTTTGCAAGAAGTTCCGGAAAGATACCAGTTGCACGACAGGGTGCATCTTTTGGGAGCTTTAGAACACAAGAAT
GTTAGAAATGTCTTAGTTCAAGGACATATTTTTCTTAATACCTCCCTTACTGAAGCATTCTGCATGGCGATCATGGAAGC
AGCCAGCTGTGGTTTACAGGTTGTAAGTACCAGGGTTGGTGGAATTCCTGAGGTGCTTCCGGAAAATCTTACTATTTTAT
GAGAAACTTCAGTAAAATCTTTGTGTGAGGGATTGGAAAAAGCTATTTTCCAACTGAAGTCAGGGGCATTGCTGGCTCCA
GAAAATATCCGTAACATAGTAAAGACTTTCTACACCTGAAGGAATGTTGTGGAGAGAACTGAAAAAGTGTATGACCAAGT
ATCGGTGGAATCTGTGTTGCCAATGGACAAACAACTGGACATACTTATTTCTCACTGTGGACCAGTAACAGGCTACATCT
TTGCTTTGTTGGCTGTTTTCAACTTCCTCTTCCTCATTTTCTTGAGATGGATGACTCCAGATTCTATCATTGATACTGGA
ATAGATGCCACTGGGCCAAGGGGTGCCTGGACTCATTAATGTTCTCACAGTAAAAGAGGGGGTGAGAATATTAAGATATC
TAAAACCAGG

Alignment

ORF - retro_ggor_828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MACRGGAGNGHRASATLSRVSPGSLYTCRTHTHNICMVSDFFYPNMGGVESHIYQLSQCLIERGHKVIIV
          MA..G..G.G...SATLS.VSPGSLYT.RTHT.NICM.SDFFYPNMGGVESHIYQL.QCLI.RG.KVIIV
Retrocopy MAYKGEGGHGQPPSATLSKVSPGSLYTRRTHTRNICMASDFFYPNMGGVESHIYQLPQCLIGRGDKVIIV

Parental  THAYGNRKGIRYLTNGLKVYYLPLKVMYNQSTATTLFHSLPLLRYIFVRERVTIIHSHSSFSAMAHDALF
          .HAYGNRKGIRYLTN.LKVY.LPLKVMYNQS.A.TLFHSLPLL..IFV.ERVTIIHSHSSFSAMA.D.LF
Retrocopy IHAYGNRKGIRYLTNDLKVYFLPLKVMYNQSMAMTLFHSLPLLKCIFVQERVTIIHSHSSFSAMAYDVLF

Parental  HAKTMGLQTVFTDHSLFGFADVSSVLTNKLLTVSLCDTNHIICVSYTSKENTVLRAALNPEIVSVIPNAV
          HAKTMGLQTV.TDH.L.GFA.V.SVLTNKLLTVSLCD...IICVSYTSKENTVLRAAL..EIVSVIPNAV
Retrocopy HAKTMGLQTVLTDHPLSGFAKVHSVLTNKLLTVSLCDASRIICVSYTSKENTVLRAALITEIVSVIPNAV

Parental  DPTDFTPDPFRRHDSITIVVVSRLVYRKGIDLLSGIIPEL-CQKYPDLNFIIGGEGPKRIILEEVRERYQ
          DPTDFTPDPFRRHDSITIVV.SRLVYRKG..L.SGIIP.L.CQKY.DLNFIIGGEGP.RIIL.EV.ERYQ
Retrocopy DPTDFTPDPFRRHDSITIVV-SRLVYRKGTNLVSGIIPKL>CQKYSDLNFIIGGEGPNRIILQEVPERYQ

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

Parental  PSVKSLCEGLEKAIFQLKSGTLPAPENVHNIVKTFYTWRNVAERTEKVYDRVSVEAVLPMDKRLDRLISH
          .SVKSLCEGLEKAIFQLKSG.L.APEN..NIVKTFYT.RNV.ERTEKVYD.VSVE.VLPMDK.LD.LISH
Retrocopy TSVKSLCEGLEKAIFQLKSGALLAPENIRNIVKTFYT*RNVVERTEKVYDQVSVESVLPMDKQLDILISH

Parental  CGPVTGYIFALLAVLNFLFLIFLRWMTPDSIIDVAIDATGPRGAWTNNYSHSKRGGENNEISETR
          CGPVTGYIFALLAV.NFLFLIFLRWMTPDSIID..IDATGPRGAWT...SHSKRGGEN..IS.TR
Retrocopy CGPVTGYIFALLAVFNFLFLIFLRWMTPDSIIDTGIDATGPRGAWTH*CSHSKRGGENIKISKTR

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	4.65 RPM
SRP007412_cerebellum	0.00 RPM	7.53 RPM
SRP007412_heart	0.00 RPM	1.09 RPM
SRP007412_kidney	0.12 RPM	6.13 RPM
SRP007412_liver	0.03 RPM	5.14 RPM
SRP007412_testis	0.41 RPM	6.01 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_828 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_828 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1050
Pan troglodytes	retro_ptro_716
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,