RetrogeneDB ID: retro_pabe_2143

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:94453630..94454357(-)
• Located in intron of: ENSPPYG00000013091

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF670
• Ensembl ID: ENSPPYG00000000040
• Aliases: None
• Description: zinc finger protein 670 [Source:HGNC Symbol;Acc:28167]

Sequence

>retro_pabe_2143
GTGACTTTTGAGGATGTGGCTGTAACCTTCACCCCCTCAGGAGTGGGCGTTGCTGGATTTTTCCCAGAAGAAACTCTTAT
AGAGATGTGACGCAGGAAACCTTCAGGAATTTGGTTTCTACAGGAAACAAATGGGAAGACCAGAATGTTGATGATCAAGT
CAGAAAATATGGGAGAAATGTAAGTCATATGGTAGAGAGACTGTGTGAAGGTAAACAAAATAGTCAAGGTGGAGAAACCT
TCAGCCAGAATTCAAATCTTAATCTAGAACAAGAAAGTTTCTACTAAAGTAAAACCATGTGTATGCAGAATTGTGTGGAA
AAGTCTTCATATGTCATGCATCTCTTCACAGGTATATTATATCTCACTCTGGACACAAACTATTTGAGTGTGAGGACTGT
GAAATGAAGCCATATAAATGTAAACAATAATGAGAAAGCCTTTAATTCTCTCACAGGTGTTTGAAGACACATGGTAATGC
ACAGTGATAACGGATTTTATAAATGTACAGTATGTGGGGAAAACTTTATTTTCCCCAGTTTATTTCAAATGCACCAGAAA
ACTCACACTGGAGAAAACAACCCTATAAATGTAAACATTGTGGTAAAGACTTCAATATTCCAGAAACTGTCACGAACATG
AAATAACTCATAGTGGAGAGAAACCCTATGCATGCAATAAAAAATGATAAATTATTAGCTTCTTCCTACACCCTTCGAGA
ACATGAA

Alignment

ORF - retro_pabe_2143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 62.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  VSFEDVAVAFTQ-EEWALLDPSQKNL-YRDVMQEIFRNLASVGNKSEDQNIQDDFKNPGRNLSSHVVERL
          V.FEDVAV.FT...EWALLD.SQK.L.YRDV.QE.FRNL.S.GNK.EDQN..D.....GRN.S.H.VERL
Retrocopy VTFEDVAVTFTP>QEWALLDFSQKKL>YRDVTQETFRNLVSTGNKWEDQNVDDQVRKYGRNVS-HMVERL

Parental  FAIKEGSQYGETFSQDSNLNL-NKKVSTGVKPCECSV-CGKVFICHSALHRHILSHTGNKLFECEECPEK
          ...K..SQ.GETFSQ.SNLNL.NKKVST.VKPC.C...CGKVFICH..LHR.I.SH.G.KLFECE.C..K
Retrocopy CEGKQNSQGGETFSQNSNLNL>NKKVSTKVKPCVCRI>CGKVFICHASLHRYIISHSGHKLFECEDCEMK

Parental  LYHCKQ-CGRAFISLTSVDRHMVTHSSNGPYKGPVYEKPFDF-PSVFQM-PQSTYTGEKTYKCKHCDKAF
          .Y.CKQ....AF.SLT.V.RHMV.HS.NG.YK..V....F.F.P..F...P.........YKCKHC.K.F
Retrocopy PYKCKQ>NEKAFNSLTGV*RHMVMHSDNGFYKCTVCGENFIF>PVYFKC>PENSHWRKQPYKCKHCGKDF

Parental  S-YSSYLREHERTHTGEKPYACK-KCGKSFTFSSSLRQHE
          ..YS....EHE.TH.GEKPYAC..K..K....S..LR.HE
Retrocopy N<YSRNCHEHEITHSGEKPYACN>KNDKLLASSYTLREHE

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	0.22 RPM
SRP007412_cerebellum	0.00 RPM	2.19 RPM
SRP007412_heart	0.06 RPM	0.33 RPM
SRP007412_kidney	0.07 RPM	0.66 RPM
SRP007412_liver	0.00 RPM	0.55 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2143 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2143 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000135747	1 retrocopy	retro_hsap_2372,
Pongo abelii	ENSPPYG00000000040	1 retrocopy	retro_pabe_2143 ,