RetrogeneDB ID: retro_hsap_3082

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:115635380..115636075(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000250215
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CIR1
• Ensembl ID: ENSG00000138433
• Aliases: CIR1, CIR
• Description: corepressor interacting with RBPJ, 1 [Source:HGNC Symbol;Acc:24217]

Sequence

>retro_hsap_3082
ATGGGGAAATCCTTCACCAACTTCATGTGCAAGAAGGACTTTCATCCCACCTCTAAATCTAATGTCAAAAAAATATGGAG
GGAGGAATAGAAAATATTACATGGTAAGAAGAAATAAGAAGAATTAATGCAACAATATCTTTAAGAACAAGAATCGTATG
ATAATAGCTTGGTTATGGGATATGAATCTGTAAAGAATGGTCTTAATTTCATGTATGAAGCCCCACCAGAAGCTTAAAAA
GTAGACAAAGAGAAAGAAGAAATAGAGGAGAGACTGAATACAAATTTGAATGGCAGAAAGGAGCCCTACAAGAAAAATAT
GCCAAAGATGACATGAACATCAGAGATCAGCCCTTTGGTATTCAGGTTTGAAATGTGAGGGGCATTAAATGTCACAAATG
GGGTCATGTCAACAGAGATCAAGAATACACTTTGTTGGGTCTTTCTGGAATCAATGCAAGTTCAGTTCCCAGTGATGGCT
CAGGGCCATCAATGCACCCCTCAGAGCCAATAGAGGAAATGAGAAACAGTGGATTTGCCCTGCAATGTAATGTACTGCAG
AGAAACTTGACCACAAATGATCCATCACAGGAGTTTGCTGTAAGTGACACTGAAGAAGATCCAGAAGTTGAATTTTTAAA
GTTATTAACAACCAAACAAAAACAGAAACTTCTCAGGAAATTAGATAAACTGGAG

Alignment

ORF - retro_hsap_3082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.69 %
• Parental protein coverage: 51.56 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKSFANFMCKKDFHPASKSNIKKVWMAEQKISYDKKKQEELMQQYLKEQESYDNRLLMGDERVKNGLNF
          MGKSF.NFMCKKDFHP.SKSN.KK.W..E.KI...KKK.EELMQQYL.EQESYDN.L.MG.E.VKNGLNF
Retrocopy MGKSFTNFMCKKDFHPTSKSNVKKIWREE*KILHGKKK*EELMQQYL*EQESYDNSLVMGYESVKNGLNF

Parental  MYEAPPGAKKENKEKEETE-GETEYKFEWQKGAPREKYAKDDMNIRDQPFGIQVRNVRCIKCHKWGHVNT
          MYEAPP.A.K..KEKEE.E.GETEYKFEWQKGA..EKYAKDDMNIRDQPFGIQV.NVR.IKCHKWGHVN.
Retrocopy MYEAPPEA*KVDKEKEEIE<GETEYKFEWQKGALQEKYAKDDMNIRDQPFGIQV*NVRGIKCHKWGHVNR

Parental  DRECPLFGLSGINASSVPTDGSGPSMHPSELIAEMRNSGFALKRNVLGRNLTANDPSQEYVASEGEEDPE
          D.E..L.GLSGINASSVP.DGSGPSMHPSE.I.EMRNSGFAL..NVL.RNLT.NDPSQE...S..EEDPE
Retrocopy DQEYTLLGLSGINASSVPSDGSGPSMHPSEPIEEMRNSGFALQCNVLQRNLTTNDPSQEFAVSDTEEDPE

Parental  VEFLKSLTTKQKQKLLRKLDRLE
          VEFLK.LTTKQKQKLLRKLD.LE
Retrocopy VEFLKLLTTKQKQKLLRKLDKLE

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	32.52 RPM
bodymap2_adrenal	0.12 RPM	52.44 RPM
bodymap2_brain	1.01 RPM	53.42 RPM
bodymap2_breast	0.00 RPM	38.11 RPM
bodymap2_colon	0.00 RPM	51.59 RPM
bodymap2_heart	0.00 RPM	20.47 RPM
bodymap2_kidney	0.00 RPM	24.88 RPM
bodymap2_liver	0.00 RPM	11.01 RPM
bodymap2_lung	0.00 RPM	33.86 RPM
bodymap2_lymph_node	0.00 RPM	23.19 RPM
bodymap2_ovary	0.00 RPM	36.49 RPM
bodymap2_prostate	0.09 RPM	41.29 RPM
bodymap2_skeletal_muscle	0.00 RPM	17.77 RPM
bodymap2_testis	0.00 RPM	70.85 RPM
bodymap2_thyroid	0.00 RPM	57.04 RPM
bodymap2_white_blood_cells	0.00 RPM	60.13 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3082 was not detected

EST

No EST(s) were mapped for retro_hsap_3082 retrocopy.

TSS

No TSS is located nearby retro_hsap_3082 retrocopy 5' end.

Lab

retro_hsap_3082 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3082 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2079
Macaca mulatta	retro_mmul_1967

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007884	1 retrocopy	retro_cjac_2152,
Homo sapiens	ENSG00000138433	2 retrocopies	retro_hsap_3082 , retro_hsap_3394,
Macaca mulatta	ENSMMUG00000023006	1 retrocopy	retro_mmul_1967,
Mustela putorius furo	ENSMPUG00000013943	1 retrocopy	retro_mputfur_178,
Mus musculus	ENSMUSG00000041777	2 retrocopies	retro_mmus_2064, retro_mmus_3104,
Nomascus leucogenys	ENSNLEG00000005869	3 retrocopies	retro_nleu_1540, retro_nleu_2013, retro_nleu_2691,
Pan troglodytes	ENSPTRG00000012652	2 retrocopies	retro_ptro_2079, retro_ptro_2306,