RetrogeneDB ID: retro_hsap_2146

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:112501689..112502239(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000228615
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CENPN
• Ensembl ID: ENSG00000166451
• Aliases: CENPN, BM039, C16orf60, CENP-N, ICEN32
• Description: centromere protein N [Source:HGNC Symbol;Acc:30873]

Sequence

>retro_hsap_2146
CAGACTGCATGTGCCTTCACTTTTTCCTCCAAGCTGAGGTGCAATAGACCGCTTCTGGGTCAGGCACTGATAATTGCTAG
CAGACAGCATCAGACTGTGAAAATGGATCTGAGAAGCTGACATCTGGACTCCCAAGCCTATTGCTTTTAAACAGTATGAT
CAGATCTTTGAAGCTGTCACAACTCGACGACACCTCTATAGGAAAGAAGCCTTGGGCTGGATATAAATATGGATTCTAGA
ATTATTCATGAAAACATAGTAGAAAAAGGAAGAGTCCAAGGAATAACTCAAAAAGCTGTTGGGGACGATCCTCAACCACA
ACTAGAATTTGCACAATTGAAGCTTGAAAGGAAATTCAAAAGTGATTTAAATGGGACCATCTTGGCTGAGAAGGAAGAAT
CCCCTTCAGTGAGTAATAAAGTTCTCTTGCTCACGTCTTTTGGAAGCAATGAAATCCTTAACCCCCGCCAGCCTTGCAGA
TAGACCGCTTTCTCCACCACTCACTTGCATATCCAGCAAGGGAATGAGTTATTTTAAAATTAGAGATAAA

Alignment

ORF - retro_hsap_2146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.91 %
• Parental protein coverage: 57.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QTPYAFTSSSMLRRNTPLLGQALTIASKHHQIVKMDLRSRYLDSLKAIVF-KQYNQTFETHNSTTPL-QE
          QT..AFT.SS.LR.N.PLLGQAL.IAS..HQ.VKMDLRS..LDS..A..F.KQY.Q.FE.......L...
Retrocopy QTACAFTFSSKLRCNRPLLGQALIIASRQHQTVKMDLRS*HLDS-QAYCF>KQYDQIFEAVTTRRHLYRK

Parental  RSLG-LDINMDSRIIHENIVEKERVQRITQETFGDYPQPQLEFAQYKLETKFKSGLNGSILAEREE-PLR
          ..LG.LDINMDSRIIHENIVEK.RVQ.ITQ...GD.PQPQLEFAQ.KLE.KFKS.LNG.ILAE.EE.PL.
Retrocopy EALG<LDINMDSRIIHENIVEKGRVQGITQKAVGDDPQPQLEFAQLKLERKFKSDLNGTILAEKEE>PLQ

Parental  CLIKFSSPHLLEALKSLAPAGIADAPLSPLLTCIPNKRMNYFKIRDK
          ..IKFS...LLEA.KSL.PA..AD.PLSP.LTCI..K.M.YFKIRDK
Retrocopy *VIKFSCSRLLEAMKSLTPASLADRPLSPPLTCISSKGMSYFKIRDK

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	4.13 RPM
bodymap2_adrenal	0.00 RPM	4.61 RPM
bodymap2_brain	0.00 RPM	5.02 RPM
bodymap2_breast	0.00 RPM	4.65 RPM
bodymap2_colon	0.00 RPM	3.60 RPM
bodymap2_heart	0.00 RPM	6.18 RPM
bodymap2_kidney	0.00 RPM	5.00 RPM
bodymap2_liver	0.00 RPM	4.58 RPM
bodymap2_lung	0.00 RPM	3.83 RPM
bodymap2_lymph_node	0.00 RPM	4.59 RPM
bodymap2_ovary	0.00 RPM	2.76 RPM
bodymap2_prostate	0.00 RPM	5.35 RPM
bodymap2_skeletal_muscle	0.00 RPM	1.49 RPM
bodymap2_testis	0.00 RPM	14.52 RPM
bodymap2_thyroid	0.04 RPM	5.88 RPM
bodymap2_white_blood_cells	0.00 RPM	3.47 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_2146 was not detected

EST

No EST(s) were mapped for retro_hsap_2146 retrocopy.

TSS

No TSS is located nearby retro_hsap_2146 retrocopy 5' end.

Lab

retro_hsap_2146 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2146 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011635	1 retrocopy	retro_btau_1101,
Felis catus	ENSFCAG00000004978	1 retrocopy	retro_fcat_1852,
Homo sapiens	ENSG00000166451	2 retrocopies	retro_hsap_2146 , retro_hsap_2291,
Oryctolagus cuniculus	ENSOCUG00000000024	3 retrocopies	retro_ocun_1676, retro_ocun_1806, retro_ocun_528,
Sarcophilus harrisii	ENSSHAG00000002111	1 retrocopy	retro_shar_331,
Ictidomys tridecemlineatus	ENSSTOG00000007345	1 retrocopy	retro_itri_1431,
Tupaia belangeri	ENSTBEG00000000039	2 retrocopies	retro_tbel_2049, retro_tbel_3055,