RetrogeneDB ID: retro_ggor_2916

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:61281620..61282241(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSGGOG00000025232
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPD
• Ensembl ID: ENSGGOG00000026760
• Aliases: None
• Description: None

Sequence

>retro_ggor_2916
AGAGTGCACCCAATCACAGGGCGATCAAGGAGTTTTGGCTTTGTGCTTTTTAAAGAATCGGAGAGTGCAGATAAGGTCAT
GGATCAAAAAGAACATAAATTGAATGGGAAGGTGATTGATCCTAAAAGGGCCAAAGTCATGAAAACAAAAGAGCCATCTA
AAAAAATTTTTGTTGGAGACCTTTCTCCAGATACACCTGAAGAGAAAATAAGGGAGTACTATGATGGTTTCAGTGAGGTG
GAATCCATAGAGCTCCCCATGGACAACAAGACCAATAAGAGGCTTGGATTCAGCTTTATTATCTTTAAGGAAGAAGAACC
AGTGAAGAAGATAAGGAAAAGGAAATACTACAATGTTGGTCTTGGTAAATGTGAATTAAAAGTAGCCATGTCAAAGGAAT
AATATCAGCAACAGCAATAGTGGGGATCTAGAGGAGGATTTGCAGGAAGAGCTCGTGGAAGAGGTGGTAGCCCCAGTCAA
AACTAGAACCAGCGATATAGTAACTATTGGAATCAAGGCTATGGCAACTATGGATATAACACCCAAGGTTATGGTGGTTA
TGGAGGATATGTCTACACTAGTTACAACAACTACTATGGATATTGTGATTATAGCAGCAGA

Alignment

ORF - retro_ggor_2916 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.02 %
• Parental protein coverage: 70.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRAKAMKTKEPVKKIFVGGLSPDTPEEKI
          ...PITGRSR.FGFVLFKESES.DKVMDQKEHKLNGKVIDPKRAK.MKTKEP.KKIFVG.LSPDTPEEKI
Retrocopy RVHPITGRSRSFGFVLFKESESADKVMDQKEHKLNGKVIDPKRAKVMKTKEPSKKIFVGDLSPDTPEEKI

Parental  REYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVAMSKEQYQQQQQ
          REY..GF.EVESIELPMDNKTNKR.GF.FI.FKEEEPVKKI...KY.NVGL.KCE.KVAMSKE.YQQQQ.
Retrocopy REYYDGFSEVESIELPMDNKTNKRLGFSFIIFKEEEPVKKIRKRKYYNVGLGKCELKVAMSKE*YQQQQ*

Parental  WGSRGGFAGRARGRGGGPSQNWNQGYSNYWNQGYGNYGYNSQGYGGYGGYDYTGYNNYYGYGDYSNQ
          WGSRGGFAGRARGRGG.PSQN.NQ.YSNYWNQGYGNYGYN.QGYGGYGGY.YT.YNNYYGY.DYS..
Retrocopy WGSRGGFAGRARGRGGSPSQN*NQRYSNYWNQGYGNYGYNTQGYGGYGGYVYTSYNNYYGYCDYSSR

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	0.10 RPM	93.13 RPM
SRP007412_cerebellum	0.08 RPM	110.75 RPM
SRP007412_heart	0.03 RPM	37.74 RPM
SRP007412_kidney	0.04 RPM	117.15 RPM
SRP007412_liver	0.03 RPM	78.82 RPM
SRP007412_testis	0.31 RPM	137.48 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_2916 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2916 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4689
Pan troglodytes	retro_ptro_3116

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015165	1 retrocopy	retro_cjac_2796,
Dipodomys ordii	ENSDORG00000012507	1 retrocopy	retro_dord_649,
Homo sapiens	ENSG00000138668	1 retrocopy	retro_hsap_4689,
Gorilla gorilla	ENSGGOG00000003040	6 retrocopies	retro_ggor_1006, retro_ggor_1010, retro_ggor_1221, retro_ggor_1738, retro_ggor_2041, retro_ggor_950,
Gorilla gorilla	ENSGGOG00000006130	6 retrocopies	retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Gorilla gorilla	ENSGGOG00000026760	1 retrocopy	retro_ggor_2916 ,
Loxodonta africana	ENSLAFG00000016483	1 retrocopy	retro_lafr_686,
Pan troglodytes	ENSPTRG00000016215	1 retrocopy	retro_ptro_3116,
Sarcophilus harrisii	ENSSHAG00000013312	1 retrocopy	retro_shar_752,
Tarsius syrichta	ENSTSYG00000010395	3 retrocopies	retro_tsyr_1092, retro_tsyr_2070, retro_tsyr_269,
Tursiops truncatus	ENSTTRG00000007592	1 retrocopy	retro_ttru_1913,
Vicugna pacos	ENSVPAG00000004374	2 retrocopies	retro_vpac_484, retro_vpac_97,