RetrogeneDB ID: retro_hsap_3438

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 6:27236241..27237008(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000270935
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDCA7
• Ensembl ID: ENSG00000144354
• Aliases: CDCA7, JPO1
• Description: cell division cycle associated 7 [Source:HGNC Symbol;Acc:14628]

Sequence

>retro_hsap_3438
GAAAGGGCTTGAAATATAAAGCAAAACAAAGCAATGCTTGTAAAACGCATGTCAGTATTAGAAGCTTCTCTGGTTTGTTC
CCCGGAAGACATTCCCCGCCAGGCCCCAACTCACAATCAAGGAGACCCCAAGGTAAACATTCCTGGATGTTTCTTCAAGG
AGACATTCTGAATGGAGAGAGCTCGGCCTCTTAGAGGTCAAGGTCAGGATCCTCGGGTCCCTTGGCGCTCTACCTACGGA
AGAGAAGGAAGAAAAGACAGAGGCTAAGTACATGTTGGTGAGAAAGAGGAAGATTGTGGACGGCTACATGAACGAAGTTG
AGATGCTCAGAAATCGTCCCGCCAGATCACCCATGATCCTTCCACATATAATTCGGCCACCGGAAGAAATTACAGAGGAA
GGTTTGGAGAACATCTGCAGCAACTCTCAAGAGAAGATATATAACCGTTCGCTGGGTTCTATTTGTCATCAATGCCGCCA
GAAAACTATTGTTATCAAACAAACTGCAGAAACCCAGACTGTTGGGGCTTTCAAGGCCTGTTCTGCGGCCCCGACCTTAG
AAACCCTTGTGGTGAAGAGGTCAGGAATACTCTGCTGGATGCGAACTGGCATTGTCCGCCTTGTCGAGGCCGTGCAACTG
CAGTTTCCGCTCGCAGCGAGATAGACTGTGGGAAACTGGGGTCCTTGAATATTTAGCCAAATACAATGGCTTTGGGAATG
TGCATGCTTACTTGAAAAGTCTGAAACAGGAATTTGAAATGCAAGCA

Alignment

ORF - retro_hsap_3438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.65 %
• Parental protein coverage: 77.51 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KRALNIKQNKAMLAKLMSELE-SFPGSFRGRHPLPGSDSQSRRPR-RRTFPGVASRRNPERRARPLTRSR
          .RA.NIKQNKAML.K.MS.LE.SF.G.F.GRH..PG..SQSRRP..R.TF..V.SRR..E.R...L....
Retrocopy ERA*NIKQNKAMLVKRMSVLE<SFSGLFPGRHSPPGPNSQSRRPQ<R*TFLDVSSRRHSEWRELGLLEVK

Parental  SRILGSLDALPMEEEEE--EDKYMLVRKRKTVDGYMNEDDLPRSRRSRSSVTLPHIIRPVEEITEEELEN
          .RILGSL.ALP.EE.EE..E.KYMLVRKRK.VDGYMNE....R.R..RS...LPHIIRP.EEITEE.LEN
Retrocopy VRILGSLGALPTEEKEEKTEAKYMLVRKRKIVDGYMNEVEMLRNRPARSPMILPHIIRPPEEITEEGLEN

Parental  VCSNSREKIYNRSLGSTCHQCRQKTIDTK-TNCRNPDCWGVRGQFCGPCLRNRYGEEVRDALLDPNWHCP
          .CSNS.EKIYNRSLGS.CHQCRQKTI..K.TNCRNPDCWG..G.FCGP.LRN..GEEVR..LLD.NWHCP
Retrocopy ICSNSQEKIYNRSLGSICHQCRQKTIVIK<TNCRNPDCWGFQGLFCGPDLRNPCGEEVRNTLLDANWHCP

Parental  PCRG-ICNCSFCRQRDGRCATGVLVYLAKYHGFGNVHAYLKSLKQEFEMQA
          PCRG..CNCSF..QRD....TGVL.YLAKY.GFGNVHAYLKSLKQEFEMQA
Retrocopy PCRG<PCNCSFRSQRDRLWETGVLEYLAKYNGFGNVHAYLKSLKQEFEMQA

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	1.65 RPM
bodymap2_adrenal	0.00 RPM	6.53 RPM
bodymap2_brain	0.00 RPM	1.66 RPM
bodymap2_breast	0.00 RPM	2.35 RPM
bodymap2_colon	0.00 RPM	14.93 RPM
bodymap2_heart	0.00 RPM	1.81 RPM
bodymap2_kidney	0.00 RPM	0.81 RPM
bodymap2_liver	0.00 RPM	0.06 RPM
bodymap2_lung	0.00 RPM	2.67 RPM
bodymap2_lymph_node	0.00 RPM	6.36 RPM
bodymap2_ovary	0.00 RPM	1.43 RPM
bodymap2_prostate	0.00 RPM	3.07 RPM
bodymap2_skeletal_muscle	0.00 RPM	6.38 RPM
bodymap2_testis	0.09 RPM	17.89 RPM
bodymap2_thyroid	0.00 RPM	1.60 RPM
bodymap2_white_blood_cells	0.00 RPM	2.64 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3438 was not detected

EST

No EST(s) were mapped for retro_hsap_3438 retrocopy.

TSS

No TSS is located nearby retro_hsap_3438 retrocopy 5' end.

Lab

retro_hsap_3438 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3438 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2331

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007809	1 retrocopy	retro_cjac_4087,
Cavia porcellus	ENSCPOG00000011784	2 retrocopies	retro_cpor_661, retro_cpor_691,
Homo sapiens	ENSG00000144354	1 retrocopy	retro_hsap_3438 ,
Mus musculus	ENSMUSG00000055612	2 retrocopies	retro_mmus_1493, retro_mmus_1494,
Nomascus leucogenys	ENSNLEG00000005787	1 retrocopy	retro_nleu_2295,
Pan troglodytes	ENSPTRG00000012645	1 retrocopy	retro_ptro_2331,
Ictidomys tridecemlineatus	ENSSTOG00000009026	1 retrocopy	retro_itri_369,

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	0.03 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).