RetrogeneDB ID: retro_ggor_1949

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:79306188..79307054(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000027576
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_ggor_1949
TTTGAGCAGAAGACGGCTGTGCCACCCACGTATGCCGATCTTGGCAAATCTGCCAGGGATGTCTTCACCAAGGGCTATGG
ATTGGCTTAATAAAGCTTGATTTGAAAACGAAATCTGAGGATGGATCGGAGTTTACAAGCTCAGGCTCAGCCAACGCTGA
GACCACCAAAGTGACGGGCAGTCTGGAAACCAGGTACCGATGGACTGACTATGGCTCGAGGTCTACGGAGAAATGGAACC
CCGGCAATACACTAGGCACCGAGATGAGCGTGGACGGTCAGCTTGCACGTGGCCTGAGGCTGACCTTGCATTCATCCTCG
TCACCTAACACTGGGAAAAAAAAAAATGCTAAAATCAAGACAGGGTGCAAGTGGGAGCACATTCACCTGGGCTGTGACGT
GGATTTCCACACTGCTGGGCCTTCCATCCAGGGTGCTCTAGTGCCGGGTTGCAGGGCTGGCTGGCTGGGTACCAGATGCG
TTTTGAGACTGCAAAGTCCTTCCTGAGTGACCCAGAGCAACTTTGCAGTTGGCTACAAGACTGATGAATTCCAGCTTCAC
ACTACTGTGAATGACGGGACAGAGTTTGGCGGCTCCATTTACCAGAAGGTGAACAAGAAGTTGCAGACCGCTGTCAATCT
CGTCTGGACAGCAGGAAACAGTAACACGCGCTTCGGAACAGCAGCCAAGTATCAGACTGACCCTCATGCCTGCTTCTCCA
CTAAAGTGAACAACTCCAGCCTGATAGGTTTAGGATACACTCAGACCCTGCAGCCAGGTATCAAACTGACACTGTCAGCT
CTCCTGGATGGCAAGAACGTCAAGGCTGGTGGCCACAAGCTTGTTCTAGGACTGAAATTTCAAGCA

Alignment

ORF - retro_ggor_1949 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.66 %
• Parental protein coverage: 97.62 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FARPMCIPPSYADLGKAARDIFNKGFGF-GLVKLDVKTKSCSGVEFSTSGSSNTDTGKVTGTLETKYKWC
          F......PP.YADLGK.ARD.F.KG.G..GL.KLD.KTKS..G.EF..SGS.N..T.KVTG.LET.Y.W.
Retrocopy FEQKTAVPPTYADLGKSARDVFTKGYGL<GLIKLDLKTKSEDGSEFTSSGSANAETTKVTGSLETRYRWT

Parental  EYGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKS-GKIKSSYKRECINLGCDVDFDFA
          .YG...TEKWN..NTLGTE.....Q...GL.LT.....SPNTG.....KIK...K.E.I.LGCDVDF..A
Retrocopy DYGSRSTEKWNPGNTLGTEMSVDGQLARGLRLTLHSSSSPNTGXXXXAKIKTGCKWEHIHLGCDVDFHTA

Parental  GPAIHGSAVFGYE-GWLAGYQMTFDSAKSKLTRNNFAVGYRTGDFQLHTNVNDGTEFGGSIYQKVCEDLD
          GP.I.G..V.G...GWL...........S..T..NFAVGY.T..FQLHT.VNDGTEFGGSIYQKV...L.
Retrocopy GPSIQGALVPGCRAGWLGTRCVLRLQSPS*VTQSNFAVGYKTDEFQLHTTVNDGTEFGGSIYQKVNKKLQ

Parental  TSVNLAWTSGTNCTRFGIAAKYQLDPTASISAKVNNSSLIGVGYTQTLRPGVKLTLSALVDGKSINAGGH
          T.VNL.WT.G...TRFG.AAKYQ.DP.A..S.KVNNSSLIG.GYTQTL.PG.KLTLSAL.DGK...AGGH
Retrocopy TAVNLVWTAGNSNTRFGTAAKYQTDPHACFSTKVNNSSLIGLGYTQTLQPGIKLTLSALLDGKNVKAGGH

Parental  KVGLALELEA
          K..L.L...A
Retrocopy KLVLGLKFQA

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	5.95 RPM	85.65 RPM
SRP007412_cerebellum	2.13 RPM	67.33 RPM
SRP007412_heart	4.03 RPM	102.03 RPM
SRP007412_kidney	3.11 RPM	115.31 RPM
SRP007412_liver	1.03 RPM	44.24 RPM
SRP007412_testis	0.52 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_1949 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1949 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2805
Pan troglodytes	retro_ptro_1900
Pongo abelii	retro_pabe_2304

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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,