RetrogeneDB ID: retro_hsap_2257

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 2:52154022..52154458(-)
• Located in intron of: ENSG00000231918

Retrocopy information

• Ensembl ID: ENSG00000226366
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CCDC12
• Ensembl ID: ENSG00000160799
• Aliases: None
• Description: coiled-coil domain containing 12 [Source:HGNC Symbol;Acc:28332]

Sequence

>retro_hsap_2257
AAAGAACAGCTGAAGGCCCTAGAGAAAACCAGGTACAGAGACAAGGAAAATGGGGAGCCAAAGACCAAGCAGCTCAGAGA
AGAGGAGGAGGAAAGCAAGAAGCTCAGGGAATTCAGGCTGCAGAACCATGTCCCAGAGGATGAGGACCTGAAAAGGAGGA
GGGTTTCCAGGCCAAACCAGTTGCAGTGGAGGAGAAGATGAAGGAGAAGCTGTAGGCAGCCAAGGCACAGCCTGTCATTG
AGGAGACGGACCTGGCCAACCTTGTACTCTAGAAGCCTGATTGGGACCTAAGAGAGATGCGGGCAAGAACCTGGAGAAAC
TAAACAAAAAGACTTGGAGGGCCATTGCCGAGCTGATCCGTGGGAGGCTAAAAGGCCCAAATGACAGCCTAGTCTCTACA
GGGGAAGCCACCACTGAACAAGAGGCCTGTGACAAC

Alignment

ORF - retro_hsap_2257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.14 %
• Parental protein coverage: 88.55 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KERLKALREKTGRKDKEDGEPKTKHLREEEEEGEKHRELRLRNYVPEDEDLKKRRVP-QAKPVAVEEKVK
          KE.LKAL.EKT...DKE.GEPKTK.LREEEEE..K.RE.RL.N.VPEDEDLK.RRV..QAKPVAVEEK.K
Retrocopy KEQLKAL-EKTRYRDKENGEPKTKQLREEEEESKKLREFRLQNHVPEDEDLKRRRVS<QAKPVAVEEKMK

Parental  EQLEAAKPEPVIEEVDLANLAPRKPDWDL-KRDVAKKLEKLKKRTQRAIAELIRERLKGQEDSLASAVDA
          E.L.AAK..PVIEE.DLANL...KPDWDL.KRD..K.LEKL.K.T.RAIAELIR.RLKG..DSL.S...A
Retrocopy EKL*AAKAQPVIEETDLANLVL*KPDWDL<KRDAGKNLEKLNKKTWRAIAELIRGRLKGPNDSLVSTGEA

Parental  ATEQKTCDS
          .TEQ..CD.
Retrocopy TTEQEACDN

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	9.88 RPM
bodymap2_adrenal	0.00 RPM	24.79 RPM
bodymap2_brain	0.00 RPM	9.42 RPM
bodymap2_breast	0.00 RPM	11.28 RPM
bodymap2_colon	0.00 RPM	11.64 RPM
bodymap2_heart	0.00 RPM	6.90 RPM
bodymap2_kidney	0.00 RPM	16.15 RPM
bodymap2_liver	0.00 RPM	8.53 RPM
bodymap2_lung	0.00 RPM	15.91 RPM
bodymap2_lymph_node	0.00 RPM	15.44 RPM
bodymap2_ovary	0.00 RPM	16.27 RPM
bodymap2_prostate	0.00 RPM	17.41 RPM
bodymap2_skeletal_muscle	0.00 RPM	9.68 RPM
bodymap2_testis	0.00 RPM	16.65 RPM
bodymap2_thyroid	0.00 RPM	19.36 RPM
bodymap2_white_blood_cells	0.00 RPM	18.98 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2257 was not detected

EST

No EST(s) were mapped for retro_hsap_2257 retrocopy.

TSS

No TSS is located nearby retro_hsap_2257 retrocopy 5' end.

Lab

retro_hsap_2257 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2257 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1597
Pongo abelii	retro_pabe_1957
Macaca mulatta	retro_mmul_1025

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002280	3 retrocopies	retro_cjac_1212, retro_cjac_2317, retro_cjac_3225,
Dipodomys ordii	ENSDORG00000016567	1 retrocopy	retro_dord_303,
Echinops telfairi	ENSETEG00000000030	2 retrocopies	retro_etel_1445, retro_etel_2038,
Homo sapiens	ENSG00000160799	1 retrocopy	retro_hsap_2257 ,
Macaca mulatta	ENSMMUG00000019810	1 retrocopy	retro_mmul_1025,
Mus musculus	ENSMUSG00000019659	1 retrocopy	retro_mmus_1275,
Nomascus leucogenys	ENSNLEG00000006219	1 retrocopy	retro_nleu_1282,
Ochotona princeps	ENSOPRG00000005086	1 retrocopy	retro_opri_746,
Pongo abelii	ENSPPYG00000013924	2 retrocopies	retro_pabe_1957, retro_pabe_2033,
Pan troglodytes	ENSPTRG00000014862	1 retrocopy	retro_ptro_1597,
Sarcophilus harrisii	ENSSHAG00000003265	1 retrocopy	retro_shar_251,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).