RetrogeneDB ID: retro_pabe_1151

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 14:20321420..20321873(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC107
• Ensembl ID: ENSPPYG00000019092
• Aliases: None
• Description: coiled-coil domain containing 107 [Source:HGNC Symbol;Acc:28465]

Sequence

>retro_pabe_1151
GATGAAGCTGCGGTTCTCCAAGAGGAGTCCGGCAAGAAGCACCCATTGCAGTTGGAGCAACAGCTGATCCAGACAGAGCA
GCACCTGGACAATCTGGTGGCCCAGCTGGACCCCCTTTTTGAGTGTGTGACTACTGTGGCTGGAGCCCCGTAGGAGCTTC
TGAACATGCAGCTACGAACCGTGAAGCTGCTAGAAGATAGCAAGCCAGATAAGGGTATGGTGGCTTCAGAACCAGAGGCC
AGCATACCTTTTCCTGAGGACTTATGTATAAAGGAAGATGAGGAGGAGGCTGCTGATGGTCAGACCTGGGAGGAGCCCAT
AAACTGGAGCACAGAGACATGGAAACTAGCTACTTCCTGGCAGGTGGAGCAGGTGCTAAGGAGAAGATGAAGCAAGGCTG
TGGAAAAGGGCTCCAGTCACAGCCCCAGCTGGGAAGGAGGGACAACAGCTGAG

Alignment

ORF - retro_pabe_1151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.11 %
• Parental protein coverage: 61.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EETSKQQPLQSEQQLAQLTQQLAQTEQHLNNLMAQLDPLFERVTTLAGAQQELLNMKLRTIHELLQDSKP
          .E....Q.........QL.QQL.QTEQHL.NL.AQLDPLFE.VTT.AGA..ELLNM.LRT...LL.DSKP
Retrocopy DEAAVLQEESGKKHPLQLEQQLIQTEQHLDNLVAQLDPLFECVTTVAGAP*ELLNMQLRTV-KLLEDSKP

Parental  DKDMEASEPEASRPLPEDFCLKEDEEEVGDSQASEEPTNWSTETWNLATSWEVERGLRRRCSQAVAKGPS
          DK.M.ASEPEAS.P.PED.C.KEDEEE..D.Q..EEP.NWSTETW.LATSW.VE..LRRR.S.AV.KG.S
Retrocopy DKGMVASEPEASIPFPEDLCIKEDEEEAADGQTWEEPINWSTETWKLATSWQVEQVLRRR*SKAVEKGSS

Parental  HSLGWEGGTIAE
          HS..WEGGT.AE
Retrocopy HSPSWEGGTTAE

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	0.06 RPM
SRP007412_cerebellum	0.00 RPM	0.49 RPM
SRP007412_heart	0.03 RPM	0.51 RPM
SRP007412_kidney	0.00 RPM	0.93 RPM
SRP007412_liver	0.00 RPM	1.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1151 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1151 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1151 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
Nomascus leucogenys	ENSNLEG00000004365	1 retrocopy	retro_nleu_1076,
Pongo abelii	ENSPPYG00000019092	1 retrocopy	retro_pabe_1151 ,