RetrogeneDB ID: retro_ggor_1473

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 19:23325092..23326147(-)
• Located in intron of: ENSGGOG00000023529

Retrocopy information

• Ensembl ID: ENSGGOG00000026936
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNX32
• Ensembl ID: ENSGGOG00000010801
• Aliases: None
• Description: None

Sequence

>retro_ggor_1473
AATGTAAATCTTCAAAGTGATCCTGCTCTGCTGGTGGACATTTCTGATGCCCTTAGTGAGTGGAATAAAGTAAAATTCAC
CGTTCACACAAAGAGTTTATTGCCAAATTTTAAACAAAATGAGTTTTCTGTTGTTCAGCAACATGAGCAATTTATCTGGC
TTCATGATTCCTTTGTTAAAAATGAAGACTATGCAGGTTACATCATTCCACCAGCACCACCAAGAGCTGATTTTGATGCT
TCAAGGGAAAAAGTACAGAAGCTTGGAGAAGGAGAAGGGTCAATGACAAAGGAAGAATTCACAAAGATGAAACAGGAACT
GGAAGCTGAATATTTGGGAATATCCAAGAACACAGTTGTGATGCATGAAGTGTTCCTATGTCATGTGACAGCACATCCTA
TTTTGAGAAAATATTTAAATTTCCATGTCTTCTTGGAATATAATCAAGATTTGAGTGTGCAAGGAAAAATAAAAAGAGAA
ACTTGAAGATTTCTTTAAAAACATGGTTAAATCAGCAGATGGAGTAATTGTTTCCGGAGTAAAGGATGTAGATAATTTCT
TTGAGCATGAACAAACATTTCTTTTAGAATATCATAACCGAGATAAGGATGCATCTGCTAAATCATAGAATGACAAGATC
CCACAAAAGTGCTGCAGATGATTACAATAGAATTGGTTCTTCATTATATGCTTTAGGAACTCGGGATTCTACAGATATAT
GCAAGTTTTTTCTCAAAGTTTCAGAAATGTTTGATAAAACAAGAAAAATAGAAGCATGAGTGTCTGCTGATGAGGACCTC
AAACTTTCTGACCCTTAAAAATATTACTTAAGAGAATCTCAAGCTGCTAAGGATCTCCTGTATTGAAGGTCTAGGTCACT
AGTGGATTATGAAAATGCTAATAAAGCCCTGGATAAAGCAAGAGCAAAAAATAAAGATGTTCTGCTGGCTAAAACTTCCC
AACAATTATGTAGTCAGAAATTTGAAAAAAAAAAATCTCAGTCTGCAAAACAAGAACTTATAGATTTTAAGACAAGAAGC
ATTGCTGCATTCAGG

Alignment

ORF - retro_ggor_1473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.56 %
• Parental protein coverage: 88.09 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SVDLQGDSSLQVEISDAVSERDKVKFTVQTKSCLPHFAQTEFSVVRQHEEFIWLHDAYVENEEYAGLIIP
          .V.LQ.D..L.V.ISDA.SE..KVKFTV.TKS.LP.F.Q.EFSVV.QHE.FIWLHD..V.NE.YAG.IIP
Retrocopy NVNLQSDPALLVDISDALSEWNKVKFTVHTKSLLPNFKQNEFSVVQQHEQFIWLHDSFVKNEDYAGYIIP

Parental  PAPPKPDFEASREKLQKLGEGDSSVTREEFAKMKQELEAEYLAIFKKTVAMHEVFLQRLAAHPTLRRDHN
          PAPP..DF.ASREK.QKLGEG..S.T.EEF.KMKQELEAEYL.I.K.TV.MHEVFL....AHP.LR...N
Retrocopy PAPPRADFDASREKVQKLGEGEGSMTKEEFTKMKQELEAEYLGISKNTVVMHEVFLCHVTAHPILRKYLN

Parental  FFVFLEYGQDLSVRG-KNRKELLGV-FLRNIVKSADEALITGMSGLKEVDDFFEHERTFLLEYH-TRIRD
          F.VFLEY.QDLSV.G.KN.K..L...F..N.VKSAD.......SG.K.VD.FFEHE.TFLLEYH.T.IR.
Retrocopy FHVFLEYNQDLSVQG<KNKKRNLKI<FFKNMVKSADGVIV---SGVKDVDNFFEHEQTFLLEYH>TEIRM

Parental  ACLRADRVMRAHKCLADDYIPISAALSSLGTQEVNQLRTSFLKLAELFERLRKLEGRVASDEDLKLSDML
          ..L...R..R.HK..ADDY..I...L..LGT.........FLK..E.F...RK.E..V..DEDLKLSD..
Retrocopy HLLN-HRMTRSHKSAADDYNRIGSSLYALGTRDSTDICKFFLKVSEMFDKTRKIEA*VSADEDLKLSDP*

Parental  RYYMRDSQAAKDLLYRRLRALADYENANKALDKARTRNREVRPAESHQQLCCQRF-ERLSDSAKQELMDF
          .YY.R.SQAAKDLLY.R.R.L.DYENANKALDKAR..N..V..A...QQLC.Q.F....S.SAKQEL.DF
Retrocopy KYYLRESQAAKDLLY*RSRSLVDYENANKALDKARAKNKDVLLAKTSQQLCSQKFXXXXSQSAKQELIDF

Parental  KSRRVSSFR
          K.R....FR
Retrocopy KTRSIAAFR

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	1.34 RPM	36.35 RPM
SRP007412_cerebellum	1.81 RPM	8.98 RPM
SRP007412_heart	0.91 RPM	0.09 RPM
SRP007412_kidney	4.54 RPM	0.29 RPM
SRP007412_liver	3.64 RPM	0.08 RPM
SRP007412_testis	6.11 RPM	3.42 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_1473 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1473 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000172803	1 retrocopy	retro_hsap_2045,
Gorilla gorilla	ENSGGOG00000008953	1 retrocopy	retro_ggor_829,
Gorilla gorilla	ENSGGOG00000010801	1 retrocopy	retro_ggor_1473 ,
Macaca mulatta	ENSMMUG00000019017	1 retrocopy	retro_mmul_1395,