RetrogeneDB ID: retro_ggor_1677

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2a:43103443..43104289(-)
• Located in intron of: ENSGGOG00000001690

Retrocopy information

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

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSGGOG00000005861
• Aliases: None
• Description: None

Sequence

>retro_ggor_1677
ATGGTTAAGCCTCCCACGTACGCTGATCTTGGCAAATCTGCCAGGGATGTGTTCACCAAGGGCTATGGATTTGGCTTAAT
AAAACTTGATTTGAAAACAAAATCTGAGAAGGGATTGGAATTTACAAACTTGGCTCAGCCAACACTGAGGCCACCAAAGT
GACTGGCAGCCTGCGAACCAAGTACAGATGGACCAGATATGGCCTGACAATTATGGATAAATGAAACACTGACCGCACAC
CGGGCACCGAGATTGCGTGGAGGATCAGCTTGCATGTGGACTGAAGTTGACCTTTGATTCATCGCTTGTCACCTAATGCT
GGGGGGAAAAATGCTAAAATCAAAACTGCTATAGGCAGGAGCATATCAACCTGGGTTGCACCGTGGATTTTGACATTGTT
GAGGCTTCAATCTGGGGTGCCCTAGTGCTGGGTTATGAGGGCTGGCTGGCTGGCTACCGGATGAATTTTGAGACCACAGA
GTTTTAAGAGAAGCAGAGGGACTTTACTCTTGGCTACGAGATTGATGAATTCCAGCTTCACACTTATGTGAATGACGGGG
CAGAGTTTGGCACCTTTGTTTCCCAGAGGTGAATAAGAAGTTGGAGACTGCTGTTAAGCTTGCCTGGATATCAGGAAACA
GTAACACTCACTTCAGAACAGCAGGCAAGTATCAGATGGACCCTGATGCCTGCTTCTTGGCTAAAGCGTACAACCCTAGC
CTGATAGGTTTAGGGTACTCTCAAACCGTAAAGCCAAGTATCAAGCTGATGTTGTCAGCTCAGCTGGATGGCAAGAACGT
CGATGCTGGTGGCCATGAGCTTGGTCTAGGACTAGAATTTCAAGCA

Alignment

ORF - retro_ggor_1677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.25 %
• Parental protein coverage: 96.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MCIPPSYADLGKAARDIFNKGFGFGLVKLDVKTKSCSGVEFST-SGSSNTDTGKVTGTLETKYKWCEYGL
          M..PP.YADLGK.ARD.F.KG.GFGL.KLD.KTKS..G.EF....GS.NT...KVTG.L.TKY.W..YGL
Retrocopy MVKPPTYADLGKSARDVFTKGYGFGLIKLDLKTKSEKGLEFTN<LGSANTEATKVTGSLRTKYRWTRYGL

Parental  TFTEKWNTDNTLGTEIA-IEDQICQGLKLTFDTT-FSPNTGKKSGKIKSS-YKRECINLGCDVDFDFAGP
          T...K.NTD.T.GTEIA..EDQ...GLKLTFD....SPN.G.K..KIK...Y..E.INLGC.VDFD....
Retrocopy TIMDK*NTDRTPGTEIA<VEDQLACGLKLTFDSS>LSPNAGGKNAKIKTA<YRQEHINLGCTVDFDIVEA

Parental  AIHGSAVFGYEGWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQK-VCEDLDTS
          .I.G..V.GYEGWLAGY.M.F...........F..GY....FQLHT.VNDG.EFG....Q..V...L.T.
Retrocopy SIWGALVLGYEGWLAGYRMNFETTEF*EKQRDFTLGYEIDEFQLHTYVNDGAEFGTFVSQR<VNKKLETA

Parental  VNLAWTSGTNCTRFGIAAKYQLDPTASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKSINAGGHKV
          V.LAW.SG...T.F..A.KYQ.DP.A...AK..N.SLIG.GY.QT..P..KL.LSA..DGK...AGGH..
Retrocopy VKLAWISGNSNTHFRTAGKYQMDPDACFLAKAYNPSLIGLGYSQTVKPSIKLMLSAQLDGKNVDAGGHEL

Parental  GLALELEA
          GL.LE..A
Retrocopy GLGLEFQA

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	0.19 RPM	85.65 RPM
SRP007412_cerebellum	0.00 RPM	67.33 RPM
SRP007412_heart	0.00 RPM	102.03 RPM
SRP007412_kidney	0.00 RPM	115.31 RPM
SRP007412_liver	0.00 RPM	44.24 RPM
SRP007412_testis	0.10 RPM	119.97 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_1677 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1677 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2250
Pongo abelii	retro_pabe_1960

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012975	2 retrocopies	retro_btau_1252, retro_btau_1389,
Canis familiaris	ENSCAFG00000015398	1 retrocopy	retro_cfam_376,
Callithrix jacchus	ENSCJAG00000001145	1 retrocopy	retro_cjac_2385,
Felis catus	ENSFCAG00000026943	3 retrocopies	retro_fcat_1385, retro_fcat_804, retro_fcat_815,
Homo sapiens	ENSG00000165637	1 retrocopy	retro_hsap_2114,
Gorilla gorilla	ENSGGOG00000001932	2 retrocopies	retro_ggor_1071, retro_ggor_3043,
Gorilla gorilla	ENSGGOG00000005861	5 retrocopies	retro_ggor_1677 , retro_ggor_1949, retro_ggor_2934, retro_ggor_3036, retro_ggor_425,
Gorilla gorilla	ENSGGOG00000010880	3 retrocopies	retro_ggor_693, retro_ggor_875, retro_ggor_981,
Macropus eugenii	ENSMEUG00000012995	1 retrocopy	retro_meug_30,
Myotis lucifugus	ENSMLUG00000007500	2 retrocopies	retro_mluc_1710, retro_mluc_2252,
Mustela putorius furo	ENSMPUG00000003268	1 retrocopy	retro_mputfur_354,
Mus musculus	ENSMUSG00000021771	1 retrocopy	retro_mmus_2667,
Otolemur garnettii	ENSOGAG00000030039	1 retrocopy	retro_ogar_2116,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Sarcophilus harrisii	ENSSHAG00000012048	1 retrocopy	retro_shar_325,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Tarsius syrichta	ENSTSYG00000004764	1 retrocopy	retro_tsyr_14,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,