RetrogeneDB ID: retro_ggor_1537

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 20:30381969..30382598(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000026956
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HDHD1
• Ensembl ID: ENSGGOG00000004425
• Aliases: None
• Description: None

Sequence

>retro_ggor_1537
GGCCTGCTTCTGGACACTGAAAGGTTCTGTTCAGTGGTGTTTCAAGACATATGTGATCGCTATGAAAAGGAATACACTGG
GGATGTGAAGTCCCTGGTCATGGGTAAGAAGGCGTTGGAGGTGGCGCAGGTGGTCGTGGACGTCCTGCAGCTCCTGGTGG
AAGAGGTGTTGGAAGAAAGCCAAGCCAGGCCAAGGGATGTGTTCCCCACTGCAGCGCTCATGCCAGGGGGCTGAGAAACT
CATCCTCCACCTTCAGAAACACAACATCCCCTTTGCCGTGGCCACCAGCTCAGAGTCTGCATCCTTTGAGGTGAAGACAA
GCAGGCACAAGAACTCTTCAGCCTGTTCCATCACATCATGCTGGGAGACGACCCGAAGTGAAGAACAGCAAGCCCAACCC
TGCCATATTCCTGACTTGTGCCAGGAGGTTCTCTCTTCCTCCTCCCGTGGAGGAGTGCCTTGTCTTTGAAGATGCGCCCA
ACGAGGTGGAGGCAGCCCTGGCTGCCAGGATGCAGGTGGTCATGGTTCTAGATGGAAACTTGAGCCAAGACCTGACCAGA
AAGGCCACCCTGGTGCTGAGTTCCCTGCAGGACTTCCAGCCCCAGCTGTTTGGTTTGCCCCACTATGAG

Alignment

ORF - retro_ggor_1537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.49 %
• Parental protein coverage: 99.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GLLLDTERLYSVVFQEICDRYDKKYSWDVKSLVMGKKALEAAQIIIDILQLPMSKEELVEESRTKLKEVF
          GLLLDTER..SVVFQ.ICDRY.K.Y..DVKSLVMGKKALE.AQ...D.LQL....EE..EES......VF
Retrocopy GLLLDTERFCSVVFQDICDRYEKEYTGDVKSLVMGKKALEVAQVVVDVLQLLV--EEVLEESQARPRDVF

Parental  PTAALMPG-AEKLIIHLRKHGIPFALATSSGSVSFDMKTSRHK-EFFSLFSHIVLGDDP-EVQHGKPDPD
          PTAALMPG.AEKLI.HL.KH.IPFA.ATSS.S.SF..KTSRHK.E.FSLF.HI.LGDDP.EV...KP.P.
Retrocopy PTAALMPG>AEKLILHLQKHNIPFAVATSSESASFEVKTSRHK<ELFSLFHHIMLGDDP<EVKNSKPNPA

Parental  IFLACAKRFSPPPAMEKCLVFEDAPNGVEAALAAGMQVVMVPDGNLSRDLTTKATLVLNSLQDFQPELFG
          IFL.CA.RFS.PP..E.CLVFEDAPN.VEAALAA.MQVVMV.DGNLS.DLT.KATLVL.SLQDFQP.LFG
Retrocopy IFLTCARRFSLPPPVEECLVFEDAPNEVEAALAARMQVVMVLDGNLSQDLTRKATLVLSSLQDFQPQLFG

Parental  LPPYE
          LP.YE
Retrocopy LPHYE

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	15.97 RPM
SRP007412_cerebellum	0.00 RPM	6.97 RPM
SRP007412_heart	0.00 RPM	4.60 RPM
SRP007412_kidney	0.00 RPM	17.34 RPM
SRP007412_liver	0.00 RPM	7.17 RPM
SRP007412_testis	0.00 RPM	6.01 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1537 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1537 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2469
Pongo abelii	retro_pabe_1837

---

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,