RetrogeneDB ID: retro_ptro_2669

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:169262..169667(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF11
• Ensembl ID: ENSPTRG00000041089
• Aliases: None
• Description: Pan troglodytes RING finger protein 11 (RNF11), mRNA. [Source:RefSeq mRNA;Acc:NM_001251948]

Sequence

>retro_ptro_2669
CTGAGACGCCCCACCTCAGATGACACTATTGTGCAACTGTCGACAGAGCAGGATCTTAGGCCCCTACTGCCACATCTGGA
ACAAGCTCCAGTTCCAGTCTATCACCCAGCACCTGGCCAGCCTCCGTTAGCAATAATGCTGACTGAAGAAGAACAAGTTA
GAATAGCTCAAAGACTAAGCCTTCTACAGTGTCTGCCTGAAGAAGTTTATGACCCTGGAAGAGATAAATCAGAAGAGGAG
ATGCCAGAGTGTGTGATCTGTTTACTGGAATTTGTTTGTGGGGACCCCATTCGATGTCTGCCATGCAAACACTTCTTTCA
CCTTGACTGCATAGACACATGGCTGCTGCGATCTTTCACATGTCCCTACTGCCGGGGGCCCGTGGATGCAGCGCTGTCTA
CATCC

Alignment

ORF - retro_ptro_2669 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.48 %
• Parental protein coverage: 87.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LHESQSDRASFGEGTEPDQEPPPPYQEQVPVPVYHPTPSQTRLATQLTEEEQIRIAQRIGLIQHLPKGVY
          L....SD.......TE.D..P..P..EQ.PVPVYHP.P.Q..LA..LTEEEQ.RIAQR..L.Q.LP..VY
Retrocopy LRRPTSDDTIVQLSTEQDLRPLLPHLEQAPVPVYHPAPGQPPLAIMLTEEEQVRIAQRLSLLQCLPEEVY

Parental  DPGRDGSEKKIRECVICMMDFVYGDPIRFLPCMHIYHLDCIDDWLMRSFTCPSCMEPVDAALLSS
          DPGRD.SE....ECVIC...FV.GDPIR.LPC.H..HLDCID.WL.RSFTCP.C..PVDAAL..S
Retrocopy DPGRDKSEEEMPECVICLLEFVCGDPIRCLPCKHFFHLDCIDTWLLRSFTCPYCRGPVDAALSTS

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	40.18 RPM
SRP007412_cerebellum	0.00 RPM	52.02 RPM
SRP007412_heart	0.00 RPM	21.28 RPM
SRP007412_kidney	0.00 RPM	25.99 RPM
SRP007412_liver	0.00 RPM	13.00 RPM
SRP007412_testis	0.00 RPM	26.24 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2669 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2669 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2669 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000006072	1 retrocopy	retro_etel_873,
Homo sapiens	ENSG00000123091	1 retrocopy	retro_hsap_3925,
Gorilla gorilla	ENSGGOG00000004919	1 retrocopy	retro_ggor_2641,
Myotis lucifugus	ENSMLUG00000004439	1 retrocopy	retro_mluc_145,
Otolemur garnettii	ENSOGAG00000011682	1 retrocopy	retro_ogar_2003,
Pongo abelii	ENSPPYG00000001361	1 retrocopy	retro_pabe_3241,
Pan troglodytes	ENSPTRG00000041089	1 retrocopy	retro_ptro_2669 ,
Ictidomys tridecemlineatus	ENSSTOG00000020072	4 retrocopies	retro_itri_1747, retro_itri_1886, retro_itri_633, retro_itri_974,
Tursiops truncatus	ENSTTRG00000010211	1 retrocopy	retro_ttru_1644,