RetrogeneDB ID: retro_ggor_1309

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:56188008..56189175(+)
• Located in intron of: ENSGGOG00000034954

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSGGOG00000004480
• Aliases: None
• Description: None

Sequence

>retro_ggor_1309
ATGAGGCCGGTGGCCCTGTTCCTGAACAGCAGCCCCAAGAACAGAAAGGTGGTTGCTGCATATGGAACTTTATCTGATTT
GCTTTCTGTGACCAGCAGTAAACTCAGCATAAAAGCCACCAGTGTGTATAATGAGAAAGGTGGACTGACTGATGATATTG
CTTTGATCAGGGATGATGATGTTTTATTTGTGGGTGAGGGAGAGCCATTTATTGATCTTCAGACAGATTCTAAGCCTCCT
GAAGGACTGTTAGGATCCCACACAGAATGGCTAACATTAAATGTTGGAGGGAGGTACTTTACAACTACATGGAGCACTTT
AGCGAATAAAGAACCTGACAGTATGCTGGCCCACATGCTTAAGAACAGAGGTGTCTAGGGAAATAAGCAAGATCATAGAG
GAGCTTTCTTAATTGACCAAAGTCCTGAGTACTTTGAACCCACTTTGAACTACTTGTGTCATGGACAGCTCATTGTAAAT
GATGGCATTAATTTATTGGGTGTGTTAGAAGAAGCAAGATTTTTTGGTATTGACTCACTGATTGAACACCTAGAAGTGGC
AATAAAGAATTCTCAATCACCAGAGGATCATTCACCAATATCTCGAAAGGAATTTGTCCGATTTTTGGTAGCAACTCCAA
CCAAGTCAGAACTGTGATGCCAGAGTTTGAACTTCAGTGGTGCTGATGTTTCTCGTTAGGACCTTCGATACATTAACTTC
AAAATGGCCAATTTAAGCCGCTGCAATCTTGTACATGCAAATCTTTACTGTGCAAATCTTGAATGAGGTGATCTCTCTGG
ATCAGTGCTTGACTGTGCAAATCTCCAGGGGGTCAAGATGCTCTGTTCTAATGCAGAAGGAGCATCCCTGAAACTGTGTA
ATTTTGAGGATCTTTCTGGTCTTAAAGCCAATTTAGAAGGTGCTAATCTGAAAGGTGTGGATATGGAAGGAAGTCAGATG
ACAGGAATTAACCTGAGACTGGCTACCTTAAAAAATGCAAAGTTGAAGAATTGTAACCTCAGAGGAGCAACTCTGGCAGG
AACCGATTTAGAGAACTGTGATCTGTCTGGGTGTGATCTTCAAGAAGCCAACTTGAGAGGGTCCAACATGAAGGGAGCTA
TATTTGAAGAGATGCTGACACCACTATACACGTCACAAAATGTCAGA

Alignment

ORF - retro_ggor_1309 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MRRVTLFLNGSPKNGKVVVAVYGTLSDLLSVASSKLGIKATSVYNGKGGLIDDIALIRDDDVLFVCEGEP
          MR.V.LFLN.SPKN.KVV.A.YGTLSDLLSV.SSKL.IKATSVYN.KGGL.DDIALIRDDDVLFV.EGEP
Retrocopy MRPVALFLNSSPKNRKVVAA-YGTLSDLLSVTSSKLSIKATSVYNEKGGLTDDIALIRDDDVLFVGEGEP

Parental  FIDPQTDSKPPEGLLGFHTDWLTLNVGGRYFTTTRILRSTLVNKEPDSMLAHMFKDKGVWGNKQDHRGAF
          FID.QTDSKPPEGLLG.HT.WLTLNVGGRYFTTT....STL.NKEPDSMLAHM.K..GV.GNKQDHRGAF
Retrocopy FIDLQTDSKPPEGLLGSHTEWLTLNVGGRYFTTTW---STLANKEPDSMLAHMLKNRGV*GNKQDHRGAF

Parental  LIDRSPEYFEPILNYLRHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQPPEDHSPISRKEFV
          LID.SPEYFEP.LNYL.HGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQ.PEDHSPISRKEFV
Retrocopy LIDQSPEYFEPTLNYLCHGQLIVNDGINLLGVLEEARFFGIDSLIEHLEVAIKNSQSPEDHSPISRKEFV

Parental  RFLLATPTKSELRCQGLNFSGADLSRLDLRYINFKMANLSRCNLAHANLCCANLERADLSGSVLDCANLQ
          RFL.ATPTKSEL.CQ.LNFSGAD.SR.DLRYINFKMANLSRC...............DLSGSVLDCANLQ
Retrocopy RFLVATPTKSEL*CQSLNFSGADVSR*DLRYINFKMANLSRCXXXXXXXXXXXXX*GDLSGSVLDCANLQ

Parental  GVKMLCSNAEGASLKLCNFEDPSGLKANLEGANLKGVDMEGSQMTGINLRVATLKN-KLKNCNLRGATLA
          GVKMLCSNAEGASLKLCNFED.SGLKANLEGANLKGVDMEGSQMTGINLR.ATLKN.KLKNCNLRGATLA
Retrocopy GVKMLCSNAEGASLKLCNFEDLSGLKANLEGANLKGVDMEGSQMTGINLRLATLKNAKLKNCNLRGATLA

Parental  GTDLENCDLSGCDLQEANLRGSNVKGAIFEEMLTPLHMSQSVR
          GTDLENCDLSGCDLQEANLRGSN.KGAIFEEMLTPL..SQ.VR
Retrocopy GTDLENCDLSGCDLQEANLRGSNMKGAIFEEMLTPLYTSQNVR

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	0.05 RPM	7.86 RPM
SRP007412_cerebellum	0.08 RPM	7.60 RPM
SRP007412_heart	0.03 RPM	11.32 RPM
SRP007412_kidney	0.04 RPM	9.32 RPM
SRP007412_liver	0.03 RPM	5.51 RPM
SRP007412_testis	0.10 RPM	18.13 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_1309 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1309 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3305
Pan troglodytes	retro_ptro_2166
Pongo abelii	retro_pabe_2725

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012157	1 retrocopy	retro_chof_323,
Gorilla gorilla	ENSGGOG00000004480	3 retrocopies	retro_ggor_1309 , retro_ggor_2264, retro_ggor_2791,
Gorilla gorilla	ENSGGOG00000010496	1 retrocopy	retro_ggor_1752,
Macaca mulatta	ENSMMUG00000010151	3 retrocopies	retro_mmul_1083, retro_mmul_1218, retro_mmul_2072,
Nomascus leucogenys	ENSNLEG00000016156	3 retrocopies	retro_nleu_1386, retro_nleu_2499, retro_nleu_2990,
Pongo abelii	ENSPPYG00000018452	3 retrocopies	retro_pabe_1527, retro_pabe_2725, retro_pabe_3457,