RetrogeneDB ID: retro_hsap_2294

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:91935968..91936946(-)
• Located in intron of: ENSG00000223703

Retrocopy information

• Ensembl ID: ENSG00000232531
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SETD8
• Ensembl ID: ENSG00000183955
• Aliases: SETD8, KMT5A, PR-Set7, SET07, SET8
• Description: SET domain containing (lysine methyltransferase) 8 [Source:HGNC Symbol;Acc:29489]

Sequence

>retro_hsap_2294
CCGGGCCTGGAGATGGTGGAGCGGAGGGGCCCGGGGAGGCCCCGCACCGATGGGGAGAGCGTATTTACCGGGCAGTCAAA
GATCTATTCCTACATGAGCCCGAACAAATGCTCTGGAATGCGTTTCCCCCTTCAAGAAGAGAACTCGGTTACACATCACG
AAGTCAAATGCCAGGGGAAACCATTAGCCGGAATCTACAGGAAACGAGAAGAGAAAAGAAATACTGGGAACGCAGTACAG
AGCGCCATGAAGTCCAAGAAACAGAAGATCAAAGACGCCAGGAGAGGTCCCCTGGTACCTTTTCCAAACCAAAAATCTGA
AGCAGCAGAACCTCCAAAAACTCCACCCTCATCTTGTGATTCCACCAATGCAGCCATCGCCAAGCAAGCCCTGAAAAAGC
CCATCAAGGGCAAACAGGCCCCCCGAAAAAAAGCTCAAGGAAAAACACAACAGAATCACAAACTTACGGATTTCTACCCT
GTCCGAAGGAGATCCAGGAAGAGCAAAGCCGAGCTGCAGTCTGAAGAAAGGAAAAGAATAGATGAATTGATTGAAAGTGG
GAAGGAAGAAGGAATGAAGATTGACCTCATCGATGGCAAAGGCAGGGGTGTGATTGCCACCAAGCATTTCTCCCGGGGTG
CCTTTGTGGTGGAATACCACGGGGACCTCATCGAGATCACCGACGCCAAGAAACGGGAGGCTCTGTATGCACAGGACCCT
TCCACGGGCTGCTACATGTACTATTTTCAGTATCTGAGCAAAACCTACTGCGTGGATGCAACTAGAGAGACAAATCGCCC
AGGAAGACCGATCAATCACAGCAAATGTGGGAACTGCCAAACCAAACTGCACGACATCGACGGCGTACCTCACCTCATCC
TCATCGCCTCCCAAGACATCGCGGCTGGGGAGGAGCTCCTGTATGACTATGGGGACCGCAGCAAGGCTTCCATTGAAGCC
CACCCGTGGCTGAAGCAT

Alignment

ORF - retro_hsap_2294 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.71 %
• Parental protein coverage: 92.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PGPEMVERRGPGRPRTDGENVFTGQSKIYSYMSPNKCSGMRFPLQEENSVTHHEVKCQGKPLAGIYRKRE
          PG.EMVERRGPGRPRTDGE.VFTGQSKIYSYMSPNKCSGMRFPLQEENSVTHHEVKCQGKPLAGIYRKRE
Retrocopy PGLEMVERRGPGRPRTDGESVFTGQSKIYSYMSPNKCSGMRFPLQEENSVTHHEVKCQGKPLAGIYRKRE

Parental  EKRNAGNAVRSAMKSEEQKIKDARKGPLVPFPNQKSEAAEPPKTPPSSCDSTNAAIAKQALKKPIKGKQA
          EKRN.GNAV.SAMKS..QKIKDAR.GPLVPFPNQKSEAAEPPKTPPSSCDSTNAAIAKQALKKPIKGKQA
Retrocopy EKRNTGNAVQSAMKSKKQKIKDARRGPLVPFPNQKSEAAEPPKTPPSSCDSTNAAIAKQALKKPIKGKQA

Parental  PRKKAQGKTQQNRKLTDFYPVRRSSRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQF
          PRKKAQGKTQQN.KLTDFYPVRR.SRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATK.F
Retrocopy PRKKAQGKTQQNHKLTDFYPVRRRSRKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKHF

Parental  SRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQ
          SRG.FVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNR.GR.INHSKCGNCQ
Retrocopy SRGAFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRPGRPINHSKCGNCQ

Parental  TKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH
          TKLHDIDGVPHLILIAS.DIAAGEELLYDYGDRSKASIEAHPWLKH
Retrocopy TKLHDIDGVPHLILIASQDIAAGEELLYDYGDRSKASIEAHPWLKH

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	0.02 RPM	18.57 RPM
bodymap2_adrenal	0.00 RPM	20.20 RPM
bodymap2_brain	0.05 RPM	11.65 RPM
bodymap2_breast	0.00 RPM	20.23 RPM
bodymap2_colon	0.00 RPM	15.70 RPM
bodymap2_heart	0.00 RPM	14.93 RPM
bodymap2_kidney	0.02 RPM	14.13 RPM
bodymap2_liver	0.00 RPM	7.18 RPM
bodymap2_lung	0.02 RPM	23.40 RPM
bodymap2_lymph_node	0.02 RPM	30.44 RPM
bodymap2_ovary	0.00 RPM	18.49 RPM
bodymap2_prostate	0.00 RPM	31.00 RPM
bodymap2_skeletal_muscle	0.02 RPM	14.28 RPM
bodymap2_testis	0.00 RPM	23.21 RPM
bodymap2_thyroid	0.04 RPM	25.25 RPM
bodymap2_white_blood_cells	0.08 RPM	13.35 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2294 was not detected

EST

No EST(s) were mapped for retro_hsap_2294 retrocopy.

TSS

No TSS is located nearby retro_hsap_2294 retrocopy 5' end.

Lab

retro_hsap_2294 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2294 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000183955	2 retrocopies	retro_hsap_2294 , retro_hsap_4320,
Macaca mulatta	ENSMMUG00000013514	1 retrocopy	retro_mmul_1579,
Mus musculus	ENSMUSG00000049327	2 retrocopies	retro_mmus_1459, retro_mmus_3478,
Otolemur garnettii	ENSOGAG00000031093	1 retrocopy	retro_ogar_1217,
Pongo abelii	ENSPPYG00000005085	2 retrocopies	retro_pabe_1347, retro_pabe_1381,
Pan troglodytes	ENSPTRG00000005598	1 retrocopy	retro_ptro_1622,
Rattus norvegicus	ENSRNOG00000001062	4 retrocopies	retro_rnor_1551, retro_rnor_2837, retro_rnor_38, retro_rnor_679,
Sarcophilus harrisii	ENSSHAG00000015376	2 retrocopies	retro_shar_110, retro_shar_115,
Tursiops truncatus	ENSTTRG00000015884	1 retrocopy	retro_ttru_1301,