RetrogeneDB ID: retro_pabe_1081

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13_random:8934224..8934799(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZDHHC20
• Ensembl ID: ENSPPYG00000005201
• Aliases: None
• Description: zinc finger, DHHC-type containing 20 [Source:HGNC Symbol;Acc:20749]

Sequence

>retro_pabe_1081
GACTCATGTATTCTTAAGATGGATCATCACTGTCCTTGGGTGAATAACTGTGTGGGATTTTCTAATTACAAATTCTTCCT
GCTGTTTTTATTGTATTCCCTATTATATTGCCTTTTCGTGGCTGCAACAGTTTTAGAGTACTTTATAAAATTTTGGACGA
ATGAACTGACAGATACCCGTGCAAAATTCCACGTACTTTTTCTTTTCTTTGTGTCTGCAATGTTCTTCATCAACGTCCTC
TCACTTTTCAGCTACCACTGCTGGCTAGTTGGAAAAAATAGAACAACAATAGAATCATTCTGTGCACCCACATTTTCATA
TGGACCTGATGGAAATGGTTTCTCTCTTGGATACAATAAAAATTGGAGACAAGTCTTTGGTGATGAAAAGAAATATTGGC
TACTTCCAATATTTTGAAGCTTGGGTGATGGTTGCAGTTTCTAACTCGCCTTGTGGGGATGGGTCCAGAACAAGCTTCTG
TTACAAACCAGAATGAGTATGCCAGAAGTGGCTCAAATCAGCCTTTTCCTTTCAAACCACTTAGTGAATCCAAAAAACTC
TTGTTGGACAGTGAA

Alignment

ORF - retro_pabe_1081 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.81 %
• Parental protein coverage: 52.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSCILKMDHHCPWVNNCVGFSNYKFFLLFLLYSLLYCLFVAATVLEYFIKFWTNELTDTRAKFHVLFLFF
          DSCILKMDHHCPWVNNCVGFSNYKFFLLFLLYSLLYCLFVAATVLEYFIKFWTNELTDTRAKFHVLFLFF
Retrocopy DSCILKMDHHCPWVNNCVGFSNYKFFLLFLLYSLLYCLFVAATVLEYFIKFWTNELTDTRAKFHVLFLFF

Parental  VSAMFFISVLSLFSYHCWLVGKNRTTIESFRAPTFSYGPDGNGFSLGCSKNWRQVFGDEKKYWLLPIFSS
          VSAMFFI.VLSLFSYHCWLVGKNRTTIESF.APTFSYGPDGNGFSLG..KNWRQVFGDEKKYWLLPIF.S
Retrocopy VSAMFFINVLSLFSYHCWLVGKNRTTIESFCAPTFSYGPDGNGFSLGYNKNWRQVFGDEKKYWLLPIF*S

Parental  LGDGCS-FPTRLVGMDPEQASVTNQNEYARSSGSNQPFPIKPLSESKNRLLDSE
          LGDGCS.F.TRLVGM.PEQASVTNQNEYAR.SGSNQPFP.KPLSESK..LLDSE
Retrocopy LGDGCS<FLTRLVGMGPEQASVTNQNEYAR-SGSNQPFPFKPLSESKKLLLDSE

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	20.51 RPM
SRP007412_cerebellum	0.00 RPM	40.13 RPM
SRP007412_heart	0.03 RPM	7.22 RPM
SRP007412_kidney	0.00 RPM	12.16 RPM
SRP007412_liver	0.03 RPM	12.64 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1081 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1081 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1081 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012155	2 retrocopies	retro_chof_1627, retro_chof_2008,
Cavia porcellus	ENSCPOG00000011489	1 retrocopy	retro_cpor_303,
Equus caballus	ENSECAG00000016465	1 retrocopy	retro_ecab_683,
Homo sapiens	ENSG00000180776	1 retrocopy	retro_hsap_1211,
Gorilla gorilla	ENSGGOG00000000435	2 retrocopies	retro_ggor_1003, retro_ggor_943,
Macaca mulatta	ENSMMUG00000007373	1 retrocopy	retro_mmul_1288,
Pongo abelii	ENSPPYG00000005201	1 retrocopy	retro_pabe_1081 ,
Pongo abelii	ENSPPYG00000013950	1 retrocopy	retro_pabe_2668,
Pan troglodytes	ENSPTRG00000005695	1 retrocopy	retro_ptro_829,
Tarsius syrichta	ENSTSYG00000003013	1 retrocopy	retro_tsyr_998,