RetrogeneDB ID: retro_ggor_3039

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:83004069..83004795(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SFR1
• Ensembl ID: ENSGGOG00000025713
• Aliases: None
• Description: None

Sequence

>retro_ggor_3039
GAGGTAAACCAAGATTTCATTTTCAAGATGGAAAGTCAGTCAGACTCAGCTGTGGTTTTGCCTAGTACTCCACAGGCCTT
TGTGAATCCATCATCTTACCGTACAATTAGTTCATGAAAACAACCTATGAGTGCAACACTTAAAGAAAGATTAAGGAAAA
CAAGATCTTCATTTAATTCCTGTTACAATGTGATAAAACTTCTTAAAGTAGAGAATGAAGAAAACAATCAGAACTTTTCA
GAGAAACCAGCGTATTCCACAGAGGAAAACTGTTTGGAATTTCAAGAAAATTTTAAACACATAGACAAGTGAATTTGAAG
AAATCACATATTTGAAAAATACCTTCAAGAATATCAATGTGAGTGAATCTCAGTCACTTGATTCTGTGTCATGCAGTGCT
CTCCAAAATGAGTTTGTGAATTAGAATCTTCCTAAACAAGAATTAAACGAAGAAAAAGCAAAATTGGTGAAGCAGGTTCA
GGAGAAAGAAGACTTTCTTTGGAGGCGAAATCTCGTCCAAATGTATAGATCAAAGAATGTTGATCCGTCTCAGTTACAGT
TGTTAATAAAGAAGTAGAGAAGCTGTAGCCAGCCATTGCTTTATGAGTTGTAGTCAGCTATGTCTGAAGAGAACAAGAAA
GTAAACCTACTCAATTGATAGACCACTATGGGTTAGATAATAAATTGCTACACTGTAACAGAAGTGAAGAAGAATTTATA
GGTGTT

Alignment

ORF - retro_ggor_3039 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.33 %
• Parental protein coverage: 85.16 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKNQDFTFKMEGPSDSAVVLPSTPQASANPSSPYTNSSRKQPMSATLRERLRKTRFSFNSSYNVVKRLKV
          E.NQDF.FKME..SDSAVVLPSTPQA..NPSS..T.SS.KQPMSATL.ERLRKTR.SFNS.YNV.K.LKV
Retrocopy EVNQDFIFKMESQSDSAVVLPSTPQAFVNPSSYRTISS*KQPMSATLKERLRKTRSSFNSCYNVIKLLKV

Parental  ESEENDQTFSEKPASSTEENCLEFQESFKHID-SEFEENTNLKNTLKNLNVCESQSLDSGSCSALQNEFV
          E.EEN.Q.FSEKPA.STEENCLEFQE.FKHID.SEFEE.T.LKNT.KN.NV.ESQSLDS.SCSALQNEFV
Retrocopy ENEENNQNFSEKPAYSTEENCLEFQENFKHID>SEFEEITYLKNTFKNINVSESQSLDSVSCSALQNEFV

Parental  NEKLPKQRLNDEKAKLVKQVQEKEDLLRRLKLVKMYRSKN-DLSQLQLLIKKWRSCSQLLLYELQSAVSE
          N..LPKQ.LN.EKAKLVKQVQEKED.L.R..LV.MYRSKN.D.SQLQLLIKK.RSCSQ.LLYEL.SA.SE
Retrocopy N*NLPKQELNEEKAKLVKQVQEKEDFLWRRNLVQMYRSKNVDPSQLQLLIKK*RSCSQPLLYEL*SAMSE

Parental  ENKKLSL-TQLIDHYGLDDKLLHYNRSEEEFIDV
          ENKK..L.TQLIDHYGLD.KLLH.NRSEEEFI.V
Retrocopy ENKKVNL<TQLIDHYGLDNKLLHCNRSEEEFIGV

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	0.53 RPM
SRP007412_cerebellum	0.00 RPM	1.06 RPM
SRP007412_heart	0.00 RPM	0.28 RPM
SRP007412_kidney	0.00 RPM	0.78 RPM
SRP007412_liver	0.00 RPM	0.55 RPM
SRP007412_testis	0.00 RPM	6.22 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_3039 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3039 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2606

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000005386	2 retrocopies	retro_ecab_726, retro_ecab_887,
Echinops telfairi	ENSETEG00000015444	1 retrocopy	retro_etel_1418,
Gorilla gorilla	ENSGGOG00000025713	1 retrocopy	retro_ggor_3039 ,
Macaca mulatta	ENSMMUG00000015327	1 retrocopy	retro_mmul_2606,
Pteropus vampyrus	ENSPVAG00000004202	1 retrocopy	retro_pvam_742,