RetrogeneDB ID: retro_ggor_2838

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:30361477..30362760(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ME2
• Ensembl ID: ENSGGOG00000010823
• Aliases: None
• Description: Malic enzyme [Source:UniProtKB/TrEMBL;Acc:G3R5I4]

Sequence

>retro_ggor_2838
ATGTTGTCCGGGTTAAGCGTAGTTTCCACCACTTGTACTTTGGCATGTCTACATTTACACATAAAAGAAAAAGGCAAGCC
ACTTATGCTGAATCCAAGAACAAACAAGGGAATGGCATTTACTTTACAAGAACGACAAATGCTTGGTCTTCAAGGGCTTC
TACCTCCCCAAATACAGACATAAGATATTCAAGCCTTACGATTCCATAGAAACTTGAAAAAAATGACTAGGCTTTCGGAA
AAATATATCTACATAATGGGAATACAAGAAAGAAATGATAAATTGTTTTATAGAATACTGCAAGATGACACTGAGAGTTT
AATGCCAATTGTATATACACCGACGGTTGGTCTTGTCTGCTCCCAGTGTGGACACCTCTTTAGAAGACCTAAGGGATTAT
TTATTTCCATCTCAGACAGAGGTCATGTTAGATCAGTTGTGGATAAGTGGCCAGAAAGTCATGTTAAGGCTGTTTTAGTG
ACTGATGGAGAGAGAATTCTGGGTCTTGGAGATCTGGGTGTCTATGGAATGGGAATTCCAGTAGGAAAAATTTGTTTGTA
TACAGTTTGTCCAGGAATATGGCCTGATAGATGCCTTCTGGTGTGTATTGATGTGGGAACTGATAATATAACAGTCTTAA
AAGACACATTTTACACGGGCTTGTACCAGAAACGAGATCACACACAACAGTCTGATGATCTGATTGATGAGTTTATGAAA
GCTATTACTGACAGATATGGTTGGAACACACTCATTCAATTTGAAGGTTTTGGAAATCATAATGCATTCAGGTTCTTGAG
AAAATACCAATAAAAATGTTGCACTTTCAATGATGATATTCAAGGGACAGCTGCAGTAGCTCTAGTAGGTCTTCTTGCAA
CACAAAAAGTTACTAGTAAACCAATCTCCGAACACAAAATCTTATTCCTTGGAGCAGGAGAGATTACTCTTAGAATTGCA
AATCTTGTAGTATGTCTATGGTAGAAAATGGCCTGTCAGAAGAAGAGGCACAAAAGAAAATCTGGATGTTTGACAAGTAT
GGTTTATTAGTTTAGGGGCGGAAAGCAAAAATAGATTGTTATCAGGAACCATTTACTTACCCAGTCCCAGAGAGCATACC
TGATACTTTTGAAGATGCAGTGAATATAATGAAGACTTCAACTACAATTGGAGTTGCAGGTGCTGGCCGTCTTTTCACTC
CTAATGTAATCAGAGCCATTGGCTCTATCAATGAAAGGCCTGTAATATTTGCATTAAGTAATCCTACAGCACAGGCGGAG
TGC

Alignment

ORF - retro_ggor_2838 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.41 %
• Parental protein coverage: 73.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLSRLRVVSTTCTLACRHLHIKEKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPKIETQDIQALRFHR
          MLS.L.VVSTTCTLAC.HLHIKEKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPP.I.T.DIQALRFHR
Retrocopy MLSGLSVVSTTCTLACLHLHIKEKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPQIQT*DIQALRFHR

Parental  NLKKMTSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLACSQYGHIFRRPKGLFISISDR
          NLKKMT...EKYIYIMGIQERN.KLFYRILQDD.ESLMPIVYTPTVGL.CSQ.GH.FRRPKGLFISISDR
Retrocopy NLKKMTRLSEKYIYIMGIQERNDKLFYRILQDDTESLMPIVYTPTVGLVCSQCGHLFRRPKGLFISISDR

Parental  GHVRSIVDNWPENHVKAVVVTDGERILGLGDLGVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNI
          GHVRS.VD.WPE.HVKAV.VTDGERILGLGDLGVYGMGIPVGK.CLYT.C.GI.PDRCL.VCIDVGTDNI
Retrocopy GHVRSVVDKWPESHVKAVLVTDGERILGLGDLGVYGMGIPVGKICLYTVCPGIWPDRCLLVCIDVGTDNI

Parental  ALLKDPFYMGLYQKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREKYCTFNDDI
          ..LKD.FY.GLYQKRD.TQQ.DDLIDEFMKAITDRYG.NTLIQFE.FGNHNAFRFLRKY..K.CTFNDDI
Retrocopy TVLKDTFYTGLYQKRDHTQQSDDLIDEFMKAITDRYGWNTLIQFEGFGNHNAFRFLRKYQ*KCCTFNDDI

Parental  QGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIV-MSMVENGLSEQEAQKKIWMFDKYGL
          QGTAAVAL.GLLA.QKV.SKPISEHKILFLGAGE..L.IANL.V.MSMVENGLSE.EAQKKIWMFDKYGL
Retrocopy QGTAAVALVGLLATQKVTSKPISEHKILFLGAGEITLRIANLVV<MSMVENGLSEEEAQKKIWMFDKYGL

Parental  LVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAMASINERPVIFAL
          LV.GRKAKID.YQEPFT...PESIPDTFEDAVNI.K.ST.IGVAGAGRLFTP.VIRA..SINERPVIFAL
Retrocopy LV*GRKAKIDCYQEPFTYPVPESIPDTFEDAVNIMKTSTTIGVAGAGRLFTPNVIRAIGSINERPVIFAL

Parental  SNPTAQAEC
          SNPTAQAEC
Retrocopy SNPTAQAEC

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	17.65 RPM
SRP007412_cerebellum	0.00 RPM	15.09 RPM
SRP007412_heart	0.00 RPM	7.57 RPM
SRP007412_kidney	0.00 RPM	18.69 RPM
SRP007412_liver	0.00 RPM	8.89 RPM
SRP007412_testis	0.00 RPM	49.83 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_2838 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2838 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4237
Pongo abelii	retro_pabe_3402
Callithrix jacchus	retro_cjac_615

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001929	1 retrocopy	retro_cjac_615,
Homo sapiens	ENSG00000082212	1 retrocopy	retro_hsap_4237,
Gorilla gorilla	ENSGGOG00000010823	1 retrocopy	retro_ggor_2838 ,
Nomascus leucogenys	ENSNLEG00000011833	1 retrocopy	retro_nleu_2307,
Pongo abelii	ENSPPYG00000009163	2 retrocopies	retro_pabe_3402, retro_pabe_3510,