RetrogeneDB ID: retro_ptro_2035

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:178708090..178709376(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSEN2
• Ensembl ID: ENSPTRG00000014633
• Aliases: None
• Description: None

Sequence

>retro_ptro_2035
GAACGCAAGATATTCTATGCTGAAATGATTAACAACAATGTGATTGTGAGGAATGCAGAGGACATTGAGCCGCTCTATGG
GGAAGGTTCTTTTGGAAAATGTATTCTTTCAAGAAGCTGTCCAACCATCACAGTTTCAGATCCTAAATTGGTTGCTAAAT
GGAAAGATATGAAGACAAACATGCCTATCATCACGTCAAAGAAGTATCAGCATAGTGTTGAGTGGGTGGCAGAGCTGATG
CGTAGACGGGGACAGGATGAGAGTGCAGTGCGCAGAATCCTCAAGGATTACTTGAATCCGCTTGAGCATCGCCCTGTGAA
AAGGAATGAACAGGTTCAAATGCATGATGAGCTTAACTCTGGAATGGTCTCCAACATGGAAGGCACAGAGGTAGGAGAGA
GACCTTCTATGATAAACGGGGACTCTGGAAAGTCAGTTGTTATGGGTGATCCCAGTGAGCCATTAGGCTGCCTGCAGGAG
GGCTCTGGGAGCGACCCGCCAACAGAAGGCTTGAGGAAAGCGTGGGAGAGGACGCTTCACCTCTGCCCCAAGCATGTTAC
TGCAAACACGATGCTCTCGTCCTCCAGTCTGGCCCTCACCGTGAGGACAGCAGCCAGCATTTTGGTCTCCTGCATGCTGG
GGACAGAGGGCCTGACCAGTACGTGCTGGTGCAGGAAGCCGAGTGTGCCGTGAGCGAGAGGAAGGATGCCCCAAATGAGG
AATTGGTGCAAAGAAAGAGACTAATCTGCCGAAGAAATCCATATAGGATCTTTTGAGTATTTGCAGCTCAGCCTAGAAGA
GGCCTTCTTCCTGGTCTATGCTCTGGAATGTTTAAGTATTTGCTATGAGAAGGAGCCTTTAACGATAGCGAAGCTCTGGA
AAGCTTTCACTGTAGTTCAGCTCACGTTCAGGACCACCTACATGGCCTACCATTGCTTGCCAAGCAATGGCTAGTGCCCA
AAGTGGGGCTCAAGTACGGGACAGATTTACTGCTATATTGGAAAGGCCCTCCGTTTTACCATGCAAGCTATTCTGTCGTT
ATTGAGCTAGTTGATGAGCAGTTTGAAGGCTGTCTCTGCAGGCCTTTCAGTTGGATGTCCCTGGCTGCCTTGAGCAGAGT
TTCCGTTAATGTCTCCAAGGAACTCATGCTGTGCTGTTTCATTAAACCCTCTACTATGACTGACAAGGAAATGGAGTCAC
CAGAATGTACGAAAAAAATTAGAGTTCAGGAGGTGATTCTGAGTGGATGGGTGTCTTCATAAGAGAGGAGTGACCAAGAC
AAACTT

Alignment

ORF - retro_ptro_2035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.6 %
• Parental protein coverage: 92.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EFKIFRAEMINNNVIVRNAEDIEQLYGKGYFGKGILSRSRPSFTISDPKLVAKWKDMKTNMPIITSKRYQ
          E.KIF.AEMINNNVIVRNAEDIE.LYG.G.FGK.ILSRS.P..T.SDPKLVAKWKDMKTNMPIITSK.YQ
Retrocopy ERKIFYAEMINNNVIVRNAEDIEPLYGEGSFGKCILSRSCPTITVSDPKLVAKWKDMKTNMPIITSKKYQ

Parental  RSVEWAAELMRRQGQDESTVGRILKDYTKPLEHPPVKRDEEAQVHDELNSGMVSNMEGTAGGERPSVVNG
          .SVEW.AELMRR.GQDES.V.RILKDY..PLEH.PVKR.E..Q.HDELNSGMVSNMEGT..GERPS..NG
Retrocopy HSVEWVAELMRRRGQDESAVRRILKDYLNPLEHRPVKRNEQVQMHDELNSGMVSNMEGTEVGERPSMING

Parental  DSGKSGGVGDPREPLGCLQEGSGCHPTTES-FEKSVREDASPLPHVCCCKQDALILQRGLHHEDGSQHIG
          DSGKS...GDP.EPLGCLQEGSG..P.TE...E.SV.EDASPLP..C.CK.DAL.LQ.G.H.ED.SQH.G
Retrocopy DSGKSVVMGDPSEPLGCLQEGSGSDPPTEG<LEESVGEDASPLPQACYCKHDALVLQSGPHREDSSQHFG

Parental  LLHPGDRGPDHEYVLVEEAECAMSEREAAPNEELVQRNRLICRRNPYRI-FEYLQLSLEEAFFLVYALGC
          LLH.GDRGPD..YVLV.EAECA.SER..APNEELVQR.RLICRRNPYRI.FEYLQLSLEEAFFLVYAL.C
Retrocopy LLHAGDRGPD-QYVLVQEAECAVSERKDAPNEELVQRKRLICRRNPYRI>FEYLQLSLEEAFFLVYALEC

Parental  LSIYYEKEPLTIVKLWKAFTVVQPTFRTTYMAYHYFRSKG-WVPKVGLKYGTDLLLYRKGPPFYHASYSV
          LSI.YEKEPLTI.KLWKAFTVVQ.TFRTTYMAYH...S.G..VPKVGLKYGTDLLLY.KGPPFYHASYSV
Retrocopy LSICYEKEPLTIAKLWKAFTVVQLTFRTTYMAYHCLPSNG<LVPKVGLKYGTDLLLYWKGPPFYHASYSV

Parental  IIELVDDHFEGSLRRPLSWKSLAALSRVSVNVSKELMLCYLIKPSTMTDKEMESPECMKRIKVQEVILSR
          .IELVD..FEG.L.RP.SW.SLAALSRVSVNVSKELMLC..IKPSTMTDKEMESPEC.K.I.VQEVILS.
Retrocopy VIELVDEQFEGCLCRPFSWMSLAALSRVSVNVSKELMLCCFIKPSTMTDKEMESPECTKKIRVQEVILSG

Parental  WVSSRERSDQDDL
          WVSS.ERSDQD.L
Retrocopy WVSS*ERSDQDKL

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	0.02 RPM	10.64 RPM
SRP007412_cerebellum	0.00 RPM	16.63 RPM
SRP007412_heart	0.00 RPM	6.65 RPM
SRP007412_kidney	0.00 RPM	10.54 RPM
SRP007412_liver	0.00 RPM	4.81 RPM
SRP007412_testis	0.11 RPM	24.24 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2035 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2035 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2035 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3011
Gorilla gorilla	retro_ggor_2085
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 ,