RetrogeneDB ID: retro_pabe_1837

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20_random:5122054..5122581(-)
• Located in intron of: None

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_1837
GCTGTACCCCTGCGGCCCACCACCCACCTCCTCTTCGACATGGATGGCCTGCTTCTGGACACTGAAACGCTCTGTTCAGT
GGTGTTTCAAGACATATGTGATCGCTATGAAAACGAATACCCTGGGGATGTGAAGTCCCTGGTCATGGGTAAGAAGGCGT
TGGAGGTGGCGCAGGTGGTCGTGGACGTCCTGCAGCTCCTGGTGGTGTCCAAGGAAGAGCTGTTGGAAGAAAGCCAAGCC
AGGCCGAGGGATGTGTTCCCCACCATGGCGCTCATGCCAGGGGGCTGAGAAACTCATCCTCAACCTTCAGAAACACAACA
TCCCCTTTGCCATGGCCACCAGCTCTGAGTCTGCATCCTTCGAGGTGAAGACAAGCAGGCACAAGAACTCTTCAGCCTGT
TCCATCACATTGTGCTGGGAGATGACCCGAAGTGAAGAGCGGCAAGCCCGACCCTGCCATATTCCTGACTTGTGCCAGGA
GGTTCTCTCTGCCTCCTCCCATGGAGGAGTGCCTTGTCTTTGAAGAT

Alignment

ORF - retro_pabe_1837 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.18 %
• Parental protein coverage: 76.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  APPPQPVTHLIFDMDGLLLDTEQLYSVVFQEICDRYDKKYSWDVKSLVMGKKALEAAQIIIDVLQ-LPMS
          A.P..P.THL.FDMDGLLLDTE.L.SVVFQ.ICDRY...Y..DVKSLVMGKKALE.AQ...DVLQ.L..S
Retrocopy AVPLRPTTHLLFDMDGLLLDTETLCSVVFQDICDRYENEYPGDVKSLVMGKKALEVAQVVVDVLQLLVVS

Parental  KEELVEESQTKLKEVFPTAALMP-GAEKLIIHLRKHGIPFALATSSGSASFEMKTSHH-QEFFSLFSHIV
          KEEL.EESQ.....VFPT.ALMP.GAEKLI..L.KH.IPFA.ATSS.SASFE.KTS.H.QE.FSLF.HIV
Retrocopy KEELLEESQARPRDVFPTMALMP>GAEKLILNLQKHNIPFAMATSSESASFEVKTSRH<QELFSLFHHIV

Parental  LGDD-PEVQHGKPDPDIFLACAKRFSPPPAMEKCLVFED
          LGDD.PEV..GKPDP.IFL.CA.RFS.PP.ME.CLVFED
Retrocopy LGDD<PEVKSGKPDPAIFLTCARRFSLPPPMEECLVFED

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_1837 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1837 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1837 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2469
Gorilla gorilla	retro_ggor_1537

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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,