RetrogeneDB ID: retro_pabe_2033

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a_random:5518987..5519420(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC12
• Ensembl ID: ENSPPYG00000013924
• Aliases: None
• Description: coiled-coil domain containing 12 [Source:HGNC Symbol;Acc:28332]

Sequence

>retro_pabe_2033
AAAGAACAGCTGAAGGCCCTAGAGAAAACCAGGTACAGGGACAAGGAAAATGGGGAGCCAAAGACCAAGCAGCTCAGAGA
AGAGGAGGAGGAAAGCAAGAAGCTCAGGGAATTCAGGCTGCAGAACCATGTCCCAGAAGATGAGGACCTGAAAAGGAGGA
GGGTTTCCAGGCCAAACCAGTTGCAGTGGAGGAGAAGATGAAGGAGAAGCTGTAGGCCGCCAAGGCACAGCCTGTCACTG
AGGAGATGGACCTGGCCAACCTTGTACTCTAGAAGCCTGATTGGGACCTAAGAGAGATGTGGGCAAGAACCTGGAGAAAC
TAAACAAAATGACTCGGAGGGCCATTGCAGAGCTGATCCATGGGAGGCTAAAAGGCCCAAATGACAGCCTAGTCTCTACA
GTGGAAGCCACCACTGAACAAGAGGCCTGTGAC

Alignment

ORF - retro_pabe_2033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.62 %
• Parental protein coverage: 72.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KERLKALREKTGRKDKEDGEPKTKHLREEEEEGEKHRELRLRNYVPEDEDLKKRRVP-QAKPVAVEEKVK
          KE.LKAL.EKT...DKE.GEPKTK.LREEEEE..K.RE.RL.N.VPEDEDLK.RRV..QAKPVAVEEK.K
Retrocopy KEQLKAL-EKTRYRDKENGEPKTKQLREEEEESKKLREFRLQNHVPEDEDLKRRRVS<QAKPVAVEEKMK

Parental  EQLEAAKPEPVIEEVDLANLAPRKPDWDL-KRDVAKKLEKLKKRTQRAIAELIRERLKGQEDNLASAVDA
          E.L.AAK..PV.EE.DLANL...KPDWDL.KRDV.K.LEKL.K.T.RAIAELI..RLKG..D.L.S.V.A
Retrocopy EKL*AAKAQPVTEEMDLANLVL*KPDWDL<KRDVGKNLEKLNKMTRRAIAELIHGRLKGPNDSLVSTVEA

Parental  ATEQKACD
          .TEQ.ACD
Retrocopy TTEQEACD

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	21.01 RPM
SRP007412_cerebellum	0.00 RPM	16.90 RPM
SRP007412_heart	0.00 RPM	11.83 RPM
SRP007412_kidney	0.00 RPM	24.56 RPM
SRP007412_liver	0.00 RPM	12.24 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2033 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2033 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2033 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002280	3 retrocopies	retro_cjac_1212, retro_cjac_2317, retro_cjac_3225,
Dipodomys ordii	ENSDORG00000016567	1 retrocopy	retro_dord_303,
Echinops telfairi	ENSETEG00000000030	2 retrocopies	retro_etel_1445, retro_etel_2038,
Homo sapiens	ENSG00000160799	1 retrocopy	retro_hsap_2257,
Macaca mulatta	ENSMMUG00000019810	1 retrocopy	retro_mmul_1025,
Mus musculus	ENSMUSG00000019659	1 retrocopy	retro_mmus_1275,
Nomascus leucogenys	ENSNLEG00000006219	1 retrocopy	retro_nleu_1282,
Ochotona princeps	ENSOPRG00000005086	1 retrocopy	retro_opri_746,
Pongo abelii	ENSPPYG00000013924	2 retrocopies	retro_pabe_1957, retro_pabe_2033 ,
Pan troglodytes	ENSPTRG00000014862	1 retrocopy	retro_ptro_1597,
Sarcophilus harrisii	ENSSHAG00000003265	1 retrocopy	retro_shar_251,