RetrogeneDB ID: retro_hsap_3253

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:145376783..145377326(+)
• Located in intron of: ENSG00000156463

Retrocopy information

• Ensembl ID: ENSG00000248493
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: APOOL
• Ensembl ID: ENSG00000155008
• Aliases: None
• Description: apolipoprotein O-like [Source:HGNC Symbol;Acc:24009]

Sequence

>retro_hsap_3253
GGAAAACTGACAACCATGCCTGCAAGTCTGATACATGCATCTGTAAATGTACATGGAACCAAAGAAGAGGAATCCAAAAA
GCAGCTAGTGAAACCAGAGCAGCTCCCCGTATATACTGCACCACCGCTCCAGTCTAAATATGTTGAAGAGCAGCCTGGTC
ATTTATAAATGGGCTTTGCTTCCATCTACACTGCAACTGGTCATTATACTGGCTGGTGCAAGGATGTTTATGTCTTTGTG
AAAAATGGGATAATGGATACAGTACAATTTGGGAAAGATGCTTATGTCTATCTGAAGAATCCTCCTCGAGATTTTCTTCC
GAAAATGGGAGTTATTACGGTTTCAGGATTGGTGGGCTTGGTTTCAGCGAGAAAAGGTTTTAAGTTTAAGAAAATTACTT
ATCCTCTGGGACTGGCCACTTTATGAGCAACTGTTTGCTACCCAGTTCAGTCAGTAATAATTGCTAAGGTAACAGGGAAA
AAGGTATATGCTACAAGCCAGCAAATTTTTGAAGCAGTTAAATCATTGTGGACAAAAAGCAGC

Alignment

ORF - retro_hsap_3253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.61 %
• Parental protein coverage: 67.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKLTTMPAGLIYASVSVHAAKQEESKKQLVKPEQLPIYTAPPLQSKYVEEQPGHLQMGFASIRTATGCYI
          GKLTTMPA.LI.ASV.VH..K.EESKKQLVKPEQLP.YTAPPLQSKYVEEQPGHL.MGFASI.TATG.Y.
Retrocopy GKLTTMPASLIHASVNVHGTKEEESKKQLVKPEQLPVYTAPPLQSKYVEEQPGHL*MGFASIYTATGHYT

Parental  GWCKGVYVFVKNGIMDTVQFGKDAYVYLKNPPRDFLPKMGVITVSGLAGLVSARKGSKFKKITYPLGLAT
          GWCK.VYVFVKNGIMDTVQFGKDAYVYLKNPPRDFLPKMGVITVSGL.GLVSARKG.KFKKITYPLGLAT
Retrocopy GWCKDVYVFVKNGIMDTVQFGKDAYVYLKNPPRDFLPKMGVITVSGLVGLVSARKGFKFKKITYPLGLAT

Parental  LGATVCYPVQSVIIAKVTAKKVYATSQQIFGAVKSLWTKSS
          L.ATVCYPVQSVIIAKVT.KKVYATSQQIF.AVKSLWTKSS
Retrocopy L*ATVCYPVQSVIIAKVTGKKVYATSQQIFEAVKSLWTKSS

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
bodymap2_adipose	0.00 RPM	4.19 RPM
bodymap2_adrenal	0.00 RPM	5.20 RPM
bodymap2_brain	0.00 RPM	6.28 RPM
bodymap2_breast	0.00 RPM	5.60 RPM
bodymap2_colon	0.00 RPM	3.54 RPM
bodymap2_heart	0.00 RPM	11.58 RPM
bodymap2_kidney	0.00 RPM	4.98 RPM
bodymap2_liver	0.00 RPM	4.61 RPM
bodymap2_lung	0.00 RPM	3.39 RPM
bodymap2_lymph_node	0.00 RPM	2.12 RPM
bodymap2_ovary	0.00 RPM	3.91 RPM
bodymap2_prostate	0.00 RPM	3.93 RPM
bodymap2_skeletal_muscle	0.00 RPM	5.07 RPM
bodymap2_testis	0.02 RPM	2.45 RPM
bodymap2_thyroid	0.00 RPM	6.06 RPM
bodymap2_white_blood_cells	0.00 RPM	2.95 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3253 was not detected

EST

No EST(s) were mapped for retro_hsap_3253 retrocopy.

TSS

No TSS is located nearby retro_hsap_3253 retrocopy 5' end.

Lab

retro_hsap_3253 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3253 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2200
Gorilla gorilla	retro_ggor_2213
Pongo abelii	retro_pabe_2697
Macaca mulatta	retro_mmul_2045

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000829	1 retrocopy	retro_amel_1035,
Canis familiaris	ENSCAFG00000017383	1 retrocopy	retro_cfam_1490,
Callithrix jacchus	ENSCJAG00000008249	2 retrocopies	retro_cjac_1783, retro_cjac_2464,
Dipodomys ordii	ENSDORG00000011045	1 retrocopy	retro_dord_373,
Equus caballus	ENSECAG00000009229	1 retrocopy	retro_ecab_577,
Homo sapiens	ENSG00000155008	1 retrocopy	retro_hsap_3253 ,
Homo sapiens	ENSG00000184831	5 retrocopies