RetrogeneDB ID: retro_ggor_2085

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:186126687..186127974(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSEN2
• Ensembl ID: ENSGGOG00000012488
• Aliases: None
• Description: None

Sequence

>retro_ggor_2085
GAAAGGAAGATAGTCTATTCTGAAATGATTAACAACAATGTGATTGTGAGGAACGCAGAGGACATTGAGCCGCTCTGTGG
GGAAGGTTCTTTTGGAAAAGGTATTCTTTCAAGAAGCTGTCCAACCATCACAGTTTCAGATCCTAAATTGGTTGCTAAAT
GGAAAGATATGAAGACAAACATGCCTATCATCACGTCAAAGAAGTATCAGCGTAGTGTTGAGTGGGTGGCAGAGCTGATG
CGTAGACAGGGACAGGATGAGAGTGCAGTGCGCAGAATCCTCAAGGATTACTTGAATCCGCTTGAGCATCGCCCTGTGAA
AAGGAATGAACAGGTTCAAATGCATGATGAGCTTAACTCTGGAATGGTCTCCAACATGGAAGGCACAGCGGTAGGAGAGA
GACCTTCTATGATAAACGGGGACTCTGGAAAGTCAGTTGTTATGGGTGATCCCAGTGAGCCATTAGGCTGCCTGCAGGAG
GGCTCTGGGAGCGACCCACCAACAGAAGGCTTTGAGGAAAGCGTGGGAGAGGACGCTTCACCTCTGCCCCAAGCATGTTA
CTGCAAACACGATGCTCTCGTCCTCCAGTCTGGCTCTCACCGTGAGGACAGCAGCCAGCATTTTGGTCTCCTGCATGCTG
GGGACAGAGGGCCTGACCAGTACGTGCTGGTGCAGGAAGCCGAGTGTGCCGTGAGCGAGAGGAAGGATGCCCCAAATGAG
GAATTGGTGCAAAGAAAGAGACTAATCTGCAGAAGAAATCCATATAGGATCTTTTGAGTATTTGCAGCTCAGCCTAGAAG
AGGTCTTCTTCCTGGTCTATGCTCTGGAATGTTTAAGTATTTGCTATGAGAAGGAGCCTTTAACGATAGCGAAGCTCTGG
AAAACTTTCACTGTAGTTCAGCTTACCTTCAGGACCACCTACATGGCCTACCATTGCTTGCCAAGCAATGGCTAGTGCCC
AAAGTGGGGCTCAAGTACGGGATAGATTTACTGCTATATTGGAAAGGCCCTCCGTTTTATCATGCAAGCTATTCTGTCGT
TATTGAGCTAGTTGATGAGCAGTTTGAAGGCTGTCTCTGCAGTCCCTTCAGTTGGATGTCCCTGGCTGCCTTGAGCAGAG
TTTCCGTTAATGTCTTCAAGGAACTCATGCTGTGCTGTTTCATTAAACCCTCTACTATGACTGACAAGGAAACGGAGTCA
CCAGAATGTATGAAAAAAATTAGAGTTCAGGAGGTGATTGTGAGTTGATGGGTGTCTTCACAAGAGAGGAGTGACCAAGA
CAAACTT

Alignment

ORF - retro_ggor_2085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.85 %
• Parental protein coverage: 92.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EFKIFHAEMINNNVIVRNAEDIEQLYGKGYFGKGILSRSRPSFTISDPKLVAKWKDMKTNMPIITSKRYQ
          E.KI...EMINNNVIVRNAEDIE.L.G.G.FGKGILSRS.P..T.SDPKLVAKWKDMKTNMPIITSK.YQ
Retrocopy ERKIVYSEMINNNVIVRNAEDIEPLCGEGSFGKGILSRSCPTITVSDPKLVAKWKDMKTNMPIITSKKYQ

Parental  HSVEWAAELMRRQGQDESTVHRILKDYTKPLEHPPVKRNEEAQVHDELNSGMVSNMEGPAGGERPSVVNG
          .SVEW.AELMRRQGQDES.V.RILKDY..PLEH.PVKRNE..Q.HDELNSGMVSNMEG.A.GERPS..NG
Retrocopy RSVEWVAELMRRQGQDESAVRRILKDYLNPLEHRPVKRNEQVQMHDELNSGMVSNMEGTAVGERPSMING

Parental  DSGKSGGVGDPREPLGCLQEGSGCHPTTESLEKSVREDASPLPHVFCCKQDALILQRGLHHEDGRQHIGL
          DSGKS...GDP.EPLGCLQEGSG..P.TE..E.SV.EDASPLP....CK.DAL.LQ.G.H.ED..QH.GL
Retrocopy DSGKSVVMGDPSEPLGCLQEGSGSDPPTEGFEESVGEDASPLPQACYCKHDALVLQSGSHREDSSQHFGL

Parental  LHPGDRGPDHEYVLVEEAECAMSEREAAPNEELVRRNRLICRRNPYRI-FEYLQLSLEEAFFLVYALGCL
          LH.GDRGPD..YVLV.EAECA.SER..APNEELV.R.RLICRRNPYRI.FEYLQLSLEE.FFLVYAL.CL
Retrocopy LHAGDRGPD-QYVLVQEAECAVSERKDAPNEELVQRKRLICRRNPYRI>FEYLQLSLEEVFFLVYALECL

Parental  SIYYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHYFRSKG-WVPKVGLKYGTDLYLFLVGQIFFLNSYSVI
          SI.YEKEPLTI.KLWK.FTVVQ.TFRTTYMAYH...S.G..VPKVGLKYG.DL.L...G..F...SYSV.
Retrocopy SICYEKEPLTIAKLWKTFTVVQLTFRTTYMAYHCLPSNG<LVPKVGLKYGIDLLLYWKGPPFYHASYSVV

Parental  IELVDDHFEGSLRRPLSWKSLAALSRVSVNVSKELMLCYLIKPSTMTDKEMESPECMKRIKVQEVILSRW
          IELVD..FEG.L..P.SW.SLAALSRVSVNV.KELMLC..IKPSTMTDKE.ESPECMK.I.VQEVI.S.W
Retrocopy IELVDEQFEGCLCSPFSWMSLAALSRVSVNVFKELMLCCFIKPSTMTDKETESPECMKKIRVQEVIVS*W

Parental  VSSRERSDQDDL
          VSS.ERSDQD.L
Retrocopy VSSQERSDQDKL

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	13.91 RPM
SRP007412_cerebellum	0.00 RPM	14.07 RPM
SRP007412_heart	0.00 RPM	5.50 RPM
SRP007412_kidney	0.00 RPM	9.00 RPM
SRP007412_liver	0.00 RPM	6.15 RPM
SRP007412_testis	0.00 RPM	17.92 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_2085 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2085 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3011
Pan troglodytes	retro_ptro_2035
Pongo abelii	retro_pabe_2495
Macaca mulatta	retro_mmul_1925

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000154743	1 retrocopy	retro_hsap_3011,
Gorilla gorilla	ENSGGOG00000012488	2 retrocopies	retro_ggor_1826, retro_ggor_2085 ,
Microcebus murinus	ENSMICG00000016672	1 retrocopy	retro_mmur_883,
Macaca mulatta	ENSMMUG00000007195	1 retrocopy	retro_mmul_1925,
Pongo abelii	ENSPPYG00000013647	1 retrocopy	retro_pabe_2495,
Pan troglodytes	ENSPTRG00000014633	1 retrocopy	retro_ptro_2035,