RetrogeneDB ID: retro_hsap_1010

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:60812736..60813062(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000257865
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PAGE3
• Ensembl ID: ENSG00000204279
• Aliases: PAGE3, CT16.6, GAGED1, PAGE-3
• Description: P antigen family, member 3 (prostate associated) [Source:HGNC Symbol;Acc:4110]

Sequence

>retro_hsap_1010
ATGAGTGGGGGAAGAAGATTAACATTTAGGCTAGAGGAAGACAAAATGTACAAGAAACTTCTAAGCCAGTTGGGCCTGTG
GTTGTCCAGCAGCCCAGTGATGAACAGCCTCAAAAAGAGGAGCCACTGACTGAAAGTAAGGATGTTATGCCTGGTCAGGA
GAGAGATGAGGCGGCACCCAAGAGTCAAGGTCCTGGCTTGGAAGCTGATATTCAGGAAGTGTCTCAGGCAAAAACTGGAG
GTAAATGGGGAGATGATCCTTATGTCAAGGGTGAGATCTATCAAATTTAGAGCCTTGCTTAAGTGCTGAAAGCAGGCGAA
GGGCAA

Alignment

ORF - retro_hsap_1010 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.21 %
• Parental protein coverage: 97.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSGHQRTRSR-SRERRDDQDSNHPVGAVVAQELPSNDQLQQEEPPIESQDYTPGQERDEGALDFQVLGLA
          MSG..R...R..R.R...Q....PVG.VV.Q..PS..Q.Q.EEP..ES.D..PGQERDE.A...Q..GL.
Retrocopy MSGGRRLTFR<ARGRQNVQETSKPVGPVVVQQ-PSDEQPQKEEPLTESKDVMPGQERDEAAPKSQGPGLE

Parental  AYLWELTRSKTGGERGDGPNVKGEF-LPNLEPVKIPE-AGEGQ
          A...E....KTGG..GD.P.VKGE..L.NLEP....E.AGEGQ
Retrocopy ADIQEVSQAKTGGKWGDDPYVKGEI<LSNLEPCLSAE>AGEGQ

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	0.00 RPM
bodymap2_adrenal	0.00 RPM	0.00 RPM
bodymap2_brain	0.00 RPM	0.00 RPM
bodymap2_breast	0.00 RPM	0.00 RPM
bodymap2_colon	0.00 RPM	0.00 RPM
bodymap2_heart	0.00 RPM	0.00 RPM
bodymap2_kidney	0.00 RPM	0.00 RPM
bodymap2_liver	0.00 RPM	0.00 RPM
bodymap2_lung	0.00 RPM	0.00 RPM
bodymap2_lymph_node	0.00 RPM	0.00 RPM
bodymap2_ovary	0.00 RPM	0.00 RPM
bodymap2_prostate	0.00 RPM	0.00 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.00 RPM
bodymap2_testis	0.00 RPM	3.81 RPM
bodymap2_thyroid	0.00 RPM	0.00 RPM
bodymap2_white_blood_cells	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_1010 was not detected

EST

No EST(s) were mapped for retro_hsap_1010 retrocopy.

TSS

No TSS is located nearby retro_hsap_1010 retrocopy 5' end.

Lab

retro_hsap_1010 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1010 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000032005	1 retrocopy	retro_cfam_987,
Homo sapiens	ENSG00000204279	1 retrocopy	retro_hsap_1010 ,
Gorilla gorilla	ENSGGOG00000028520	1 retrocopy	retro_ggor_802,
Microcebus murinus	ENSMICG00000007757	2 retrocopies	retro_mmur_168, retro_mmur_396,
Mustela putorius furo	ENSMPUG00000005401	1 retrocopy	retro_mputfur_219,