RetrogeneDB ID: retro_ptro_2627

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:62175543..62176568(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NMD3
• Ensembl ID: ENSPTRG00000015586
• Aliases: None
• Description: None

Sequence

>retro_ptro_2627
AAAGCCCCTCTGAGTAAGGAACGGCTTGTGAATGCAGGCTTTGTTTGGACTGAGCCCCATTCTAAGAGATTTAAAGTTAA
ACTGACTCCAGAAAGAGGTGATGAATGGTGCTGTCCTTCAACAAGTGTTTGTGGTGGATTATGCTGTTCAGTCCCAAATA
TGTGGAGATTGCCATAGAGTAGAAGCTAAGGGTTTCTGGAGGGCTGTGATTCAAGTGAGGCAAAAGACTTTGCACAAAAA
AGCTTTCTACTATCTGGAACAGTTAATTCTGAAATATGGAAGGCATCAGAATACACTTCGTATCAAAGAGATTAATGATG
GTCTGGATTTTTATTATTCCTCAAAACCACATGCTCAGAAGATGGTCGAATTTATTCAGTATACAGTTCCCTGTAGATAC
AACGCATCCCAAAGACTGATCTCTCAGGATGTCCATAGTAATACATACAATTACAAAAGCACTTTTTCTGTGGAAATTGT
TCCAATATGCCAGGATTATGTTGTCTGTCTGTCTCCAAAACTGACACAAAGCCTGGGAAATATGAACCAGATTTGTGTGT
GTATTCGAATAACCAGTGCCATTCACCTCGTTGATCCAATCACCCTACAAGTTGCAGATATTGATGGGAGCACTTTCTGG
AGTCACTCTTTCAGTAGTTTATGTCACCCCAAACAGCTAGAGGAATTTATTGTGATGAAATGCAGCATAGTCCGAAATAT
AAAACACGGTGCAGATGCTGGAATGATATCAAAAAAAGCATACCCTCAGGGAAGTCTGGGTACAGAAGACATCTGAAATG
AATACAGATAAACAGTATTTTTGTCGTACTCATTTGGGACATCTTCTAAATCCTGGAGAGCTGGTGTTAGGGTTTGATTT
GGCCAGCTGCAATTTAAATGATGAGCATGGCAACAAAATGAACTCAGATAGAGTTCCAGATGTGGTATTAATCAAGAAGA
ACTAAGACTGGACCAAACATCAGTGATGTAGAAACTGGAAACTGAAAGAGCTTGCAGGAGAGAGA

Alignment

ORF - retro_ptro_2627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.47 %
• Parental protein coverage: 67.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KAPLSKVRLVDAGFVWTE-PHSKRLKVKLTIQKEVMNGAILQQVFVVDYVVQSQMCGDCHRVEAKDFWKA
          KAPLSK.RLV.AGFVWTE.P....LK.....QKEVMNGA.LQQVFVVDY.VQSQ.CGDCHRVEAK.FW.A
Retrocopy KAPLSKERLVNAGFVWTE>PILRDLKLN*-LQKEVMNGAVLQQVFVVDYAVQSQICGDCHRVEAKGFWRA

Parental  VIQVRQKTLHKKTFYYLEQLILKYGMHQNTLRIKEIHDGLDFYYSSKQHAQKMVEFLQCTVPCRYKASQR
          VIQVRQKTLHKK.FYYLEQLILKYG.HQNTLRIKEI.DGLDFYYSSK.HAQKMVEF.Q.TVPCRY.ASQR
Retrocopy VIQVRQKTLHKKAFYYLEQLILKYGRHQNTLRIKEINDGLDFYYSSKPHAQKMVEFIQYTVPCRYNASQR

Parental  LISQDIHSNTYNYKSTFSVEIVPICKDNVVCLSPKLAQSLGNMNQICVCIRVTSAIHLIDPNTLQVADID
          LISQD.HSNTYNYKSTFSVEIVPIC.D.VVCLSPKL.QSLGNMNQICVCIR.TSAIHL.DP.TLQVADID
Retrocopy LISQDVHSNTYNYKSTFSVEIVPICQDYVVCLSPKLTQSLGNMNQICVCIRITSAIHLVDPITLQVADID

Parental  GSTFWSHPFNSLCHPKQLEEFIVMECSIVRDIKRAAGAGMIS-KKHTLGEVWVQKTSEMNTDKQYFCRTH
          GSTFWSH.F.SLCHPKQLEEFIVM.CSIVR.IK..A.AGMIS.KKHTL.EVWVQKTSEMNTDKQYFCRTH
Retrocopy GSTFWSHSFSSLCHPKQLEEFIVMKCSIVRNIKHGADAGMIS>KKHTLREVWVQKTSEMNTDKQYFCRTH

Parental  LGHLLNPGDLVLGFDLANCNLNDEHVNKMNSDRVPDVVLIKKSYDRTKRQRRRNWKLKELARER
          LGHLLNPG.LVLGFDLA.CNLNDEH.NKMNSDRVPDVVLIKK..D.TK.Q..RNWKLKELA.ER
Retrocopy LGHLLNPGELVLGFDLASCNLNDEHGNKMNSDRVPDVVLIKKN*DWTKHQ*CRNWKLKELAGER

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	13.03 RPM
SRP007412_cerebellum	0.11 RPM	25.06 RPM
SRP007412_heart	0.00 RPM	31.33 RPM
SRP007412_kidney	0.05 RPM	25.03 RPM
SRP007412_liver	0.00 RPM	23.34 RPM
SRP007412_testis	0.42 RPM	21.60 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2627 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2627 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2627 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3855

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000169251	1 retrocopy	retro_hsap_3855,
Pan troglodytes	ENSPTRG00000015586	1 retrocopy	retro_ptro_2627 ,
Tursiops truncatus	ENSTTRG00000012938	1 retrocopy	retro_ttru_749,