RetrogeneDB ID: retro_pabe_2144

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:95072336..95073162(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF207
• Ensembl ID: ENSPPYG00000008161
• Aliases: None
• Description: zinc finger protein 207 [Source:HGNC Symbol;Acc:12998]

Sequence

>retro_pabe_2144
AAGAAGAGGAAGCAGCTGAAGCCGTGGTGCCGGTATTGTAATAGAGATTTTGGTGATGGGAAGATCCTTATACAGCACCA
AAAAGCAAAGCATTTTAAATGTCATATATGTCACAAGAAATTGTATCCAGGACCTGGCTTAGCTATTCATTGCATGCAGG
TGCATGAAGAAATAATAGATGCTGTACCAAATGCAATACCTGGGATAACAGACATAGAATTGGAAATATATGGTATGGAA
GGTATTCCAGAAAAAGGCATGGATGAAGGACGACGACTTCTTGAACAGAAAACACAAGAAAGTCAAAAAAAGAAGGAACA
AGATGATTCTGATGAATATGATGACGACGACTCTGCCGGCTCAACTTCATTTCAACCACAACCTGTTCAACTTCAACAAG
GTTATATTCCTCCAGTGGCACAGCCAGGACTGCTGCTAGTACCAGGAGCACCAGGAATGCCTCTAGGCATAACTCCATTA
ATGCCAGGTATTCCTCCTCTGATGCCAGGAATGCCACCAGTTATGCCAGCCATGCCACCTGGATTGCTTCATCAAAGAAA
ATGCACCCAGTCATTTTGCGGTGAAAACATAATGATGCCAATGGGTGGAATATACCACCTGGACCAGGAATACCACCTCT
GATGCCTGGAATGTCACCAAGTATCCCCTCCACTCCCCCACCCCCATTCCACATCCTAGAATTCCTCCAGTGACCCAAAC
ACAGGCTGTTTCAGCGCCAGGTATTCTTAACAGACCACCTGCACCAACAGCAACTGTACCTGCTCCACAGCCTCCAGTTA
TGAAGCCTCTTTTCTCCAGTGCTGGA

Alignment

ORF - retro_pabe_2144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.61 %
• Parental protein coverage: 55.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KKKKQLKPWCWYCNRDFDDEKILIQHQKAKHFKCHICHKKLYTGPGLAIHCMQVHKETIDAVPNAIPGRT
          KK.KQLKPWC.YCNRDF.D.KILIQHQKAKHFKCHICHKKLY.GPGLAIHCMQVH.E.IDAVPNAIPG.T
Retrocopy KKRKQLKPWCRYCNRDFGDGKILIQHQKAKHFKCHICHKKLYPGPGLAIHCMQVHEEIIDAVPNAIPGIT

Parental  DIELEIYGMEGIPEKDMDERRRLLEQKTQESQKKKQQDDSDEYDDDDSAASTSFQPQPVQPQQGYIPPMA
          DIELEIYGMEGIPEK.MDE.RRLLEQKTQESQKKK.QDDSDEYDDDDSA.STSFQPQPVQ.QQGYIPP.A
Retrocopy DIELEIYGMEGIPEKGMDEGRRLLEQKTQESQKKKEQDDSDEYDDDDSAGSTSFQPQPVQLQQGYIPPVA

Parental  QPGLPPVPGAPGMPPGIPPLMPGVPPLMPGMPPVMPGMPPGLHHQRKYTQSFCGENIMMPMGGM-MPPGP
          QPGL..VPGAPGMP.GI.PLMPG.PPLMPGMPPVMP.MPPGL.HQRK.TQSFCGENIMMPMGG...PPGP
Retrocopy QPGLLLVPGAPGMPLGITPLMPGIPPLMPGMPPVMPAMPPGLLHQRKCTQSFCGENIMMPMGGI<IPPGP

Parental  GIPPLMPGMPPGMP----PP-VPRPGIPPMTQAQAVSAPGILNRPPAPTATVPAPQPPVTKPLFPSAG
          GIPPLMPGM.P..P....PP..P.P.IPP.TQ.QAVSAPGILNRPPAPTATVPAPQPPV.KPLF.SAG
Retrocopy GIPPLMPGMSPSIPSTPPPP<IPHPRIPPVTQTQAVSAPGILNRPPAPTATVPAPQPPVMKPLFSSAG

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	36.44 RPM
SRP007412_cerebellum	0.00 RPM	51.56 RPM
SRP007412_heart	0.00 RPM	24.38 RPM
SRP007412_kidney	0.03 RPM	36.96 RPM
SRP007412_liver	0.03 RPM	38.37 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2144 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2144 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001728	1 retrocopy	retro_cpor_1464,
Echinops telfairi	ENSETEG00000003828	1 retrocopy	retro_etel_883,
Homo sapiens	ENSG00000010244	1 retrocopy	retro_hsap_2373,
Myotis lucifugus	ENSMLUG00000016085	1 retrocopy	retro_mluc_322,
Nomascus leucogenys	ENSNLEG00000005954	1 retrocopy	retro_nleu_362,
Otolemur garnettii	ENSOGAG00000001200	2 retrocopies	retro_ogar_33, retro_ogar_751,
Pongo abelii	ENSPPYG00000008161	1 retrocopy	retro_pabe_2144 ,
Pan troglodytes	ENSPTRG00000008989	1 retrocopy	retro_ptro_1735,
Ictidomys tridecemlineatus	ENSSTOG00000000712	2 retrocopies	retro_itri_1800, retro_itri_1875,