RetrogeneDB ID: retro_ptro_3116

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:63571092..63571713(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPD
• Ensembl ID: ENSPTRG00000016215
• Aliases: HNRNPD, HNRPD
• Description: Heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa) [Source:UniProtKB/TrEMBL;Acc:K7D7U2]

Sequence

>retro_ptro_3116
AGAGTGCACCCAATCACAGGGCGATCAAGGAGTTTTGGCTTTGTGCTTTTTAAAGAATCAGAGAGTGCAGATAAGGTCAT
GGATCAAAAAGAACATAAATTGAATGGGAATGTGATTGATCCTAAAAGGGCCAAAGTCATGAAAACAAAAGAGCCATCTA
AAAAAATTTTTGTTGGAGACCTTTCTCCAGATACACCTGAAGAGAAAATAAGGGAGTACTATGATGGTTTCAGTGAGGTG
GAATCCATAGAGCTCCCCATGGACAACAAGACCAATAAGAGGCTTGGATTCAGCTTTATTATCTTTAAGGAAGAAGAACA
AGTGAAGAAGATAATGAAAAGGAAATACTACAATGTTGGTCTTGGTAAATGTGAATTAAAAGTAGCCATGTCAAAGGAAT
AATATCAGCAACAGCAATAGTGGGGATCTAGAGGAGGATTTGCAGGAAGAGCTCGTGGAAGAGGTGGTGGCCCCAGTCAA
AACTAGAACCAGCGATATAGTAACTATTGGAATCAAGGCTATGGCAACTATGGATATAACACCCAAGGTTATGGTGGTTA
TGGAGGATATGTCTACACTAGTTACAACAACTACTATGGATATTGTGATTATAGCAGCAGA

Alignment

ORF - retro_ptro_3116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.02 %
• Parental protein coverage: 58.31 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLDPITGRSRGFGFVLFKESESVDKVMDQKEHKLNGKVIDPKRAKAMKTKEPVKKIFVGGLSPDTPEEKI
          ...PITGRSR.FGFVLFKESES.DKVMDQKEHKLNG.VIDPKRAK.MKTKEP.KKIFVG.LSPDTPEEKI
Retrocopy RVHPITGRSRSFGFVLFKESESADKVMDQKEHKLNGNVIDPKRAKVMKTKEPSKKIFVGDLSPDTPEEKI

Parental  REYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVGLSKCEIKVAMSKEQYQQQQQ
          REY..GF.EVESIELPMDNKTNKR.GF.FI.FKEEE.VKKIM..KY.NVGL.KCE.KVAMSKE.YQQQQ.
Retrocopy REYYDGFSEVESIELPMDNKTNKRLGFSFIIFKEEEQVKKIMKRKYYNVGLGKCELKVAMSKE*YQQQQ*

Parental  WGSRGGFAGRARGRGGGPSQNWNQGYSNYWNQGYGNYGYNSQGYGGYGGYDYTGYNNYYGYGDYSNQ
          WGSRGGFAGRARGRGGGPSQN.NQ.YSNYWNQGYGNYGYN.QGYGGYGGY.YT.YNNYYGY.DYS..
Retrocopy WGSRGGFAGRARGRGGGPSQN*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	0.02 RPM	73.57 RPM
SRP007412_cerebellum	0.07 RPM	152.28 RPM
SRP007412_heart	0.00 RPM	79.77 RPM
SRP007412_kidney	0.03 RPM	104.29 RPM
SRP007412_liver	0.00 RPM	111.03 RPM
SRP007412_testis	0.32 RPM	129.73 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3116 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3116 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3116 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4689
Gorilla gorilla	retro_ggor_2916

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 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	ENSGGOG00000026760	1 retrocopy	retro_ggor_2916,
Loxodonta africana	ENSLAFG00000016483	1 retrocopy	retro_lafr_686,
Pan troglodytes	ENSPTRG00000012676	5 retrocopies	retro_ptro_1059, retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Pan troglodytes	ENSPTRG00000016215	1 retrocopy	retro_ptro_3116 ,
Pan troglodytes	ENSPTRG00000017601	1 retrocopy	retro_ptro_666,
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,