RetrogeneDB ID: retro_pabe_280

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:99427055..99427568(+)
• Located in intron of: ENSPPYG00000000847

Retrocopy information

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

Parental gene information

• Parental gene symbol: HDHD1
• Ensembl ID: ENSPPYG00000020105
• Aliases: None
• Description: haloacid dehalogenase-like hydrolase domain containing 1 [Source:HGNC Symbol;Acc:16818]

Sequence

>retro_pabe_280
CCCCCACTGCAGCCCATCATCCACCTCATCTTTGACATGGATGGCCTTCTTCTGGATACTGAAGGGCTATATTCATTGCT
GTTTCAAGAAATATGTGATTGCTATGAAAAGAAATACAGCTGGGATGTAAAGTCCCTGGTAATGGGTAAGTAGGCATTAG
AGGCAGCACAGATTATAAGAGACATCTTGCAGCTCCTGATGTCCAAGGAGGAGCTGGTGGAATAAAGCCAAACGAAGTTA
AAGGAAGTGTTCCCTACAGCTGTGCTCATGCCAGGGACTGAGAATCTCATCGTCCGCCTGCAGAAACACAGCATTCCCTT
TGCCATGGCCACCAGCTCAGGGTCTGCCTCATTGGAGATGAAGGTGAGCCAACACAAGGAGTTTTTCAGGTTGTTTTCTC
ACATTATGCTGGGAGATGACCCCAAAGTACAGCACAGCAAGCCAGACCCCAACATTGTCCTAGCTTATGCCAAGAGGTTC
TCTCCCTGTCCTACTACGGAGAAGTGCCTTGTT

Alignment

ORF - retro_pabe_280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.53 %
• Parental protein coverage: 74.67 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPPQPVTHLIFDMDGLLLDTEQLYSVVFQEICDRYDKKYSWDVKSLVMGKKALEAAQIIIDVLQLPMSKE
          PP.QP..HLIFDMDGLLLDTE.LYS..FQEICD.Y.KKYSWDVKSLVMGK.ALEAAQII.D.LQL.MSKE
Retrocopy PPLQPIIHLIFDMDGLLLDTEGLYSLLFQEICDCYEKKYSWDVKSLVMGK*ALEAAQIIRDILQLLMSKE

Parental  ELVEESQTKLKEVFPTAALMPGAEKLIIHLRKHGIPFALATSSGSASFEMKTSHHQEFFSLFSHIVLGDD
          ELVE.SQTKLKEVFPTA.LMPG.E.LI..L.KH.IPFA.ATSSGSAS.EMK.S.H.EFF.LFSHI.LGDD
Retrocopy ELVE*SQTKLKEVFPTAVLMPGTENLIVRLQKHSIPFAMATSSGSASLEMKVSQHKEFFRLFSHIMLGDD

Parental  PEVQHGKPDPDIFLACAKRFSPPPAMEKCLV
          P.VQH.KPDP.I.LA.AKRFSP.P..EKCLV
Retrocopy PKVQHSKPDPNIVLAYAKRFSPCPTTEKCLV

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	14.21 RPM
SRP007412_cerebellum	0.00 RPM	8.15 RPM
SRP007412_heart	0.00 RPM	2.50 RPM
SRP007412_kidney	0.00 RPM	15.58 RPM
SRP007412_liver	0.00 RPM	14.96 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_280 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_280 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_280 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_454

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004616	1 retrocopy	retro_acar_48,
Choloepus hoffmanni	ENSCHOG00000001318	5 retrocopies	retro_chof_1597, retro_chof_1855, retro_chof_1883, retro_chof_2136, retro_chof_2168,
Homo sapiens	ENSG00000130021	2 retrocopies	retro_hsap_2469, retro_hsap_454,
Gorilla gorilla	ENSGGOG00000004425	1 retrocopy	retro_ggor_1537,
Microcebus murinus	ENSMICG00000017082	1 retrocopy	retro_mmur_1321,
Macaca mulatta	ENSMMUG00000017377	1 retrocopy	retro_mmul_244,
Monodelphis domestica	ENSMODG00000017505	2 retrocopies	retro_mdom_1374, retro_mdom_52,
Pongo abelii	ENSPPYG00000020105	2 retrocopies	retro_pabe_1837, retro_pabe_280 ,
Pteropus vampyrus	ENSPVAG00000011149	1 retrocopy	retro_pvam_1165,
Tarsius syrichta	ENSTSYG00000013238	4 retrocopies	retro_tsyr_2013, retro_tsyr_345, retro_tsyr_542, retro_tsyr_931,