RetrogeneDB ID: retro_pabe_981

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:19709831..19710448(+)
• Located in intron of: ENSPPYG00000005193

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35E1
• Ensembl ID: ENSPPYG00000009692
• Aliases: None
• Description: solute carrier family 35, member E1 [Source:HGNC Symbol;Acc:20803]

Sequence

>retro_pabe_981
GCTGCCACGCTGTGCTTCTTGCTTCAGAACATTTTCTCCAAAAAGATATTGAGAGATTTGTGGATCCACCATCTCCCGCT
GCTCAACATCTTGGGCTGCGACGCTGTCTTTTTTATGATCCCCACCTGGGTTCTGGTGGACCTCTCAGCTTTCCTGGTCA
GCAGCGACTTGACTACGTCTCCCAGTGGCCCTGGATGCTCCTGCTTCTGGCTGTCAGTGGCTTCTGTAACTTTGCCCAGA
ATGTCATCGCCTTTAGCATCCTCAACCTCGTCAGCTCCCTGAGCTATTCGGTCGTCAATGCCACCAGGAGAATCATGGTC
ATCACAGTGTCCCTGATCATGCTGCCCAATGCAGTCACCAGCACCAATGTCCTGGGCATAATAACTGCCATCCTCGGGGT
CTTCCTCTACAACAAGACCAAGTAAGATGCAAACCAGCAAGTCAGGAAGCACCTCCTGCTGGCACCACAGTGGACCTGAG
CAGCAAGGAGCATCACCAGAGCCCGCTGGAGAAGCCCCACCAATGGCCTCCTCTTCCCCCAGCATGGGGACTATCATGGC
TCCAATAATATCTTAACAGACCACTTCCAGTACAGCTGGCAGAGCTACCCAAACTCG

Alignment

ORF - retro_pabe_981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 77.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AATLCFSLQNIFSKKVLRDSRIHHLRLLNILGCHAVFFMIPTWVLVDLSAFLVSSDLT-YVYQWPWTLLL
          AATLCF.LQNIFSKK.LRD..IHHL.LLNILGC.AVFFMIPTWVLVDLSAFLVSSDLT.YV.QWPW.LLL
Retrocopy AATLCFLLQNIFSKKILRDLWIHHLPLLNILGCDAVFFMIPTWVLVDLSAFLVSSDLT<YVSQWPWMLLL

Parental  LAVSGFCNFAQNVIAFSILNLVSPLSYSVANATKRIMVITVSLIMLRNPVTSTNVLGMMTAILGVFLYNK
          LAVSGFCNFAQNVIAFSILNLVS.LSYSV.NAT.RIMVITVSLIML.N.VTSTNVLG..TAILGVFLYNK
Retrocopy LAVSGFCNFAQNVIAFSILNLVSSLSYSVVNATRRIMVITVSLIMLPNAVTSTNVLGIITAILGVFLYNK

Parental  TKYDANQQARKHLLPV-TTADLSGKERHRSPLEKPH-NGLLFPQHGDYQYGRNNILTDHFQYSRQSYPNS
          TK.DANQQ.RKHLL...TT.DLS.KE.H.SPLEKPH.NGLLFPQHGDY..G.NNILTDHFQYS.QSYPNS
Retrocopy TK*DANQQVRKHLLLA<TTVDLSSKEHHQSPLEKPH>NGLLFPQHGDY-HGSNNILTDHFQYSWQSYPNS

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	0.06 RPM	23.11 RPM
SRP007412_cerebellum	0.00 RPM	17.63 RPM
SRP007412_heart	0.00 RPM	8.07 RPM
SRP007412_kidney	0.10 RPM	15.98 RPM
SRP007412_liver	0.03 RPM	14.57 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_981 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_981 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_981 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000127526	1 retrocopy	retro_hsap_1170,
Nomascus leucogenys	ENSNLEG00000005563	1 retrocopy	retro_nleu_2854,
Pongo abelii	ENSPPYG00000009692	1 retrocopy	retro_pabe_981 ,
Pan troglodytes	ENSPTRG00000010648	1 retrocopy	retro_ptro_804,