RetrogeneDB ID: retro_pabe_2818

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5_random:16286517..16287542(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC86
• Ensembl ID: ENSPPYG00000003205
• Aliases: None
• Description: coiled-coil domain-containing protein 86 [Source:RefSeq peptide;Acc:NP_001127360]

Sequence

>retro_pabe_2818
TCCTCAGTTTCGTGGGCGAGATTGGCCCTTGTGGAGTTCGAGTCCAACCCAGAAGAAACAAGGAAGCCTGGGTCTCCTCC
AGGTGTGCAGCAACCCAGCCTGGGGTCCCCCCAAAGGTAGCCAGGGACAAGCCCAGGATCACCCAGTCTGCAGCAGGGTG
CAAAGGTTTGGGGTCCCCCACAAAGGCAGCCAGAGCCAAGCCCAGGGTCCCCCGAGCATCAGCAAGATCTATACCTGGAG
TCACCTCAAAGACAGCTAGAGTCTAGCTCTGAATCCCCACAATGTCAGCGAAAGCCAAGTGAGGAGGCATCACGGTGTTC
TCAGGGCCAGGGAGAACCAGCCTCCGAGTGGGCCCAGAGTCCAGAGGAGCTGACCCCGGGGGTGGGGTGGCATGAGCACC
TATACCCAGGCCCAGGATCACCAGAGCCTTACCCCAGTCAGCAAGTGCTGAGTTCAGAGCCATCACGGCCAGTACGGGAG
CTGACACCCAAGGCACCTGGCTCCCTGCTGGGATCAGCAGGAGCCAAGCAAGCTGCCTCTGGCTGGGGAGAGGTAACAGG
TGGCCATGGGTCAAAGAAGGAAAAAGGTTCTTCAGCCCAGGCTCCAGTATCCAAGAAGTTGAAGGAGGTGGAGGAGGAGT
TTCCTGTAATCCAGAAGGGGAGGCCCAAATTGGGGTGGGTGTGGAAGGACCACTGCAAGAAAAAGTTATCCCAGATGGTT
CAGGGCAAGCCCCTGCACACATCCTGGCAGTGGAAGATGAAGGAACAGCAGGAAAGGAAGCTTGCCAAGGATTCTGCCCC
TAACCTGGAGAAGGAGAAGGAAAGGCACTGCCAGGAGAAGAAACAGCGCTGGGCCAAGAACCTGAAACATCACCTGTAGA
ACGAGTGGAAGGCGGAGATTGTCCAAGTGATCCAAAGCCCCACCAAGCTTAAGCTGGCGAGGACACAGCAGCTGTGCTCC
ATGAGAAGCGGGACACCCTGCCCCTGCTGCAGAACCGGCCGTCCCAGCAGCCAGCAGCCAAGGTC

Alignment

ORF - retro_pabe_2818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 93.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TSVSRTRRALVELESNPEETREPGSPPSVQRAGLGSPERPPKTSPGSPRLQQGSGLESP-QGQPEPGAGS
          .SVS..R.ALVE.ESNPEETR.PGSPP.VQ...LGSP.R.P.TSPGSP.LQQG.....P.Q.QPEP..GS
Retrocopy SSVSWARLALVEFESNPEETRKPGSPPGVQQPSLGSPQR*PGTSPGSPSLQQGAKVWGPPQRQPEPSPGS

Parental  PQRQQDLHLESPQRQPEYSPESPRCQPKPSEEVPKCSQDQGVLASELAQSKEELTPGAPQHQ-LPPVPGS
          P..QQDL.LESPQRQ.E.S.ESP.CQ.KPSEE...CSQ.QG..ASE.AQS.EELTPG...H..L.P.PGS
Retrocopy PEHQQDLYLESPQRQLESSSESPQCQRKPSEEASRCSQGQGEPASEWAQSPEELTPGVGWHEHLYPGPGS

Parental  PEPYPGQQAPGPEPSQPLLELTPRAPGSPRG-QHEPSKPPPAGET-VTGGFGAKKRKGSSSQAPASKKLN
          PEPYP.QQ....EPS.P..ELTP.APGS..G.Q.EPSK.P.AGE..VTGG.G.KK.KGSS.QAP.SKKL.
Retrocopy PEPYPSQQVLSSEPSRPVRELTPKAPGSLLG>QQEPSKLPLAGER<VTGGHGSKKEKGSSAQAPVSKKLK

Parental  K--EELPVIPKGKPKSGRVWKDRSKKRFSQMLQDKPLRTSWQRKMKERQERKLAKDFARHLEEEKERRRQ
          ...EE.PVI.KG.PK.G.VWKD..KK..SQM.Q.KPL.TSWQ.KMKE.QERKLAKD.A..LE.EKER..Q
Retrocopy EVEEEFPVIQKGRPKLGWVWKDHCKKKLSQMVQGKPLHTSWQWKMKEQQERKLAKDSAPNLEKEKERHCQ

Parental  EKKQRRAENLKRRLENERKAEVVQVIRNPAKLKRAKKKQLRSI-EKRDTLALLQKQPPQRPAAKI
          EKKQR.A.NLK..L.NE.KAE.VQVI..P.KLK.A...QL.S..EKRDTL.LLQ..P.Q.PAAK.
Retrocopy EKKQRWAKNLKHHL*NEWKAEIVQVIQSPTKLKLARTQQLCSM<EKRDTLPLLQNRPSQQPAAKV

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	7.13 RPM
SRP007412_cerebellum	0.00 RPM	5.35 RPM
SRP007412_heart	0.00 RPM	3.61 RPM
SRP007412_kidney	0.00 RPM	16.67 RPM
SRP007412_liver	0.00 RPM	7.62 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2818 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2818 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2818 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110104	2 retrocopies	retro_hsap_3276, retro_hsap_3834,
Gorilla gorilla	ENSGGOG00000013670	1 retrocopy	retro_ggor_2582,
Macaca mulatta	ENSMMUG00000000019	1 retrocopy	retro_mmul_1622,
Nomascus leucogenys	ENSNLEG00000013582	1 retrocopy	retro_nleu_2131,
Pongo abelii	ENSPPYG00000003205	1 retrocopy	retro_pabe_2818 ,
Pan troglodytes	ENSPTRG00000003721	2 retrocopies	retro_ptro_2216, retro_ptro_2610,