RetrogeneDB ID: retro_pabe_2140

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:93555675..93556188(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DAZAP2
• Ensembl ID: ENSPPYG00000004524
• Aliases: None
• Description: DAZ-associated protein 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R526]

Sequence

>retro_pabe_2140
ATGAACAGCAAAGGTCAATATCCAACACAGCCAACCTAGCCTGTGCAGCCTCCTGGGAATCCAGTATACCCTCAGACCTT
GCATCTTTCTCAGGCTCCACCCTATACTGATGCTCCAACTGCCTACTCAGAGCTCTATCATCCAAGCTTTGTGCACCCAG
GGGCTGCCACAGTCCCCACCACGTCGGCCACATTTCCTGGAGCCTCTCTGTATCTTCCCATGGCCCAGTCTGTGGGCTGT
TGGGGTCTTTAGGTTCCACAATCCCCATGGCTTATTTACCCAGTTGGTCCCATCTATCCACCTGGCTCCACAGTGCCTGG
TGGAAGGAGGGTATGATGCAGATGCCAGATTTTGGAGCTGGGGCTACTGCTGGCAACATTCCTCCCTCCACCTCCTGGGA
TGCCCTCCCTAGTGCTGCTCAGCTTGGCAGTCATGCAGGGAGCCAACGTCCTCGTAACTCAGTGGAATGGGAACTTCTTC
ATGGATGGATCAGATGGTGGCTACACCATCTGG

Alignment

ORF - retro_pabe_2140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.14 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  MNSKGQYPTQPTYPVQPPGNPVYPQTLHLPQAPPYTDAPPAYSELYRPSFVHPGAATVPTMSAAFPGASL
          MNSKGQYPTQPT.PVQPPGNPVYPQTLHL.QAPPYTDAP.AYSELY.PSFVHPGAATVPT.SA.FPGASL
Retrocopy MNSKGQYPTQPT*PVQPPGNPVYPQTLHLSQAPPYTDAPTAYSELYHPSFVHPGAATVPTTSATFPGASL

Parental  YLPMAQSV-AVG-PLGSTIPMAY-YPVGPIYPPGSTV-LVEGGYDAGAR-FGAGATAGNIP-PPPP-GCP
          YLPMAQSV.AVG..LGSTIPMAY.YPVGPIYPPGSTV.LVEGGYDA.AR.FGAGATAGNIP.PPPP.GCP
Retrocopy YLPMAQSV>AVG>SLGSTIPMAY>YPVGPIYPPGSTV>LVEGGYDADAR>FGAGATAGNIP>PPPP>GCP

Parental  -PNAAQ-LAVMQGANVLVTQRKGNFFMGGSDGGYTIW
          .P.AAQ.LAVMQGANVLVTQ..GNFFM.GSDGGYTIW
Retrocopy >PSAAQ>LAVMQGANVLVTQWNGNFFMDGSDGGYTIW

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	0.06 RPM	84.48 RPM
SRP007412_cerebellum	0.12 RPM	92.05 RPM
SRP007412_heart	0.00 RPM	56.08 RPM
SRP007412_kidney	0.03 RPM	184.26 RPM
SRP007412_liver	0.03 RPM	83.79 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2140 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2140 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2140 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2370
Gorilla gorilla	retro_ggor_1800
Macaca mulatta	retro_mmul_958

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017661	2 retrocopies	retro_cjac_636, retro_cjac_793,
Homo sapiens	ENSG00000183283	1 retrocopy	retro_hsap_2370,
Gorilla gorilla	ENSGGOG00000026861	1 retrocopy	retro_ggor_1800,
Myotis lucifugus	ENSMLUG00000009959	1 retrocopy	retro_mluc_351,
Macaca mulatta	ENSMMUG00000001884	1 retrocopy	retro_mmul_958,
Nomascus leucogenys	ENSNLEG00000017776	1 retrocopy	retro_nleu_360,
Otolemur garnettii	ENSOGAG00000007977	3 retrocopies	retro_ogar_2109, retro_ogar_2139, retro_ogar_3130,
Pongo abelii	ENSPPYG00000004524	1 retrocopy	retro_pabe_2140 ,