RetrogeneDB ID: retro_pabe_547

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:90047486..90048314(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000009810
• Aliases: None
• Description: None

Sequence

>retro_pabe_547
ACGGTTCCGCTGCGCGCCCCGGATGTGGCGCGGCTGCGCGAGGAGCAGGAAAAGGTGGTCACTAACTGCCAAGAGAGAAT
CCAGCATTGGAAGAAGGTAGATAATGACTATAATGCCCTTCGAGAAAGACTCAGCACCTTGCCTGATAAATTGTCTTATA
ATATAATGGTACCATTTGGCCCTTTTGCCTTCATGCCAGGAAAACTTGTCCATACTAATGAAGTCACTGTTTTACTGGGG
GACAACTGGTTTGCAAAGTGCTCAGCAAAGCAGGCTGTAGGTTTAGTTGAGCACCGAAAAGAACATGTAAGAAAAACAAT
AGATGACTTAAAAAAAGTGATGAAAACTTTTGAATCCAGAGTTGAATTCACGGAAGATTTGCAGAAAATGAGTGATGCTG
CAGGTGATATTGTTGACATAAGAGAAGAAATTAAATGTGACTTCGAATTTAAAGCAAAACACCGAATTGCTCATAAACCG
CATTCCAAACCAAAAACTTCAGATATTTTTGAAGCAGATATTGCAAATGACGTGAAATCCAAGGATTTGCTAGCTGATAA
AGAACTGTGGGCTCGACTTGAAGAACTAGAAAGACAAGAAGAATTGCTGGGTGAACTTGATAGTAAGCCTGATACTGTGA
TTGCAAATGGAGAAGATACGACATCTTCTGAAGAGGAAAAGGAAGATCATAACACAAATGTGAATGCGATGCATCAAGTA
ACAGACTCTCATACTCCTTGTTATAAGGATGTTGCAAGTTCAGAACCATTCAGTGGTCAAGTGAATAGTCAGTTGAACTG
TTCAGTGAATGGTTCCAGTTCTTACCAC

Alignment

ORF - retro_pabe_547 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.19 %
• Parental protein coverage: 50.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TVPLRAPDVARLREEQEKVVTNCQERIQHWKKVDNDYNALRERLSTLPDKLSYNIMVPFGPFAFMPGKLV
          TVPLRAPDVARLREEQEKVVTNCQERIQHWKKVDNDYNALRERLSTLPDKLSYNIMVPFGPFAFMPGKLV
Retrocopy TVPLRAPDVARLREEQEKVVTNCQERIQHWKKVDNDYNALRERLSTLPDKLSYNIMVPFGPFAFMPGKLV

Parental  HTNEVTVLLGDNWFAKCSAKQAVGLVEHRKEHVRKTIDDLKKVMKNFESRVEFTEDLQKMSDAAGDIVDI
          HTNEVTVLLGDNWFAKCSAKQAVGLVEHRKEHVRKTIDDLKKVMK.FESRVEFTEDLQKMSDAAGDIVDI
Retrocopy HTNEVTVLLGDNWFAKCSAKQAVGLVEHRKEHVRKTIDDLKKVMKTFESRVEFTEDLQKMSDAAGDIVDI

Parental  REEIKCDFEFKAKHRIAHKPHSKPKTSDIFEAVTANDVKSKDLLADKELWARLEELERQEELLGELDSKP
          REEIKCDFEFKAKHRIAHKPHSKPKTSDIFEA..ANDVKSKDLLADKELWARLEELERQEELLGELDSKP
Retrocopy REEIKCDFEFKAKHRIAHKPHSKPKTSDIFEADIANDVKSKDLLADKELWARLEELERQEELLGELDSKP

Parental  DTVIANGEDTTSSEEEKEDHNTNVNVMHQVTDSHTPCHKDVASSEPFSGQVNSQLNCSVNGSSSYH
          DTVIANGEDTTSSEEEKEDHNTNVN.MHQVTDSHTPC.KDVASSEPFSGQVNSQLNCSVNGSSSYH
Retrocopy DTVIANGEDTTSSEEEKEDHNTNVNAMHQVTDSHTPCYKDVASSEPFSGQVNSQLNCSVNGSSSYH

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	11.83 RPM
SRP007412_cerebellum	0.00 RPM	13.86 RPM
SRP007412_heart	0.06 RPM	6.47 RPM
SRP007412_kidney	0.00 RPM	13.03 RPM
SRP007412_liver	0.06 RPM	10.47 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_547 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_547 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_547 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
Callithrix jacchus	ENSCJAG00000001823	1 retrocopy	retro_cjac_2693,
Monodelphis domestica	ENSMODG00000012675	1 retrocopy	retro_mdom_1513,
Pongo abelii	ENSPPYG00000009810	1 retrocopy	retro_pabe_547 ,
Pan troglodytes	ENSPTRG00000010784	1 retrocopy	retro_ptro_3086,