RetrogeneDB ID: retro_hsap_3396

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:157413535..157414389(-)
• Located in intron of: ENSG00000253743

Retrocopy information

• Ensembl ID: ENSG00000213414
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDC37
• Ensembl ID: ENSG00000105401
• Aliases: CDC37, P50CDC37
• Description: cell division cycle 37 [Source:HGNC Symbol;Acc:1735]

Sequence

>retro_hsap_3396
GAGGATCGGAGCTGGGAGCAGAAGCTGGAGGAGATGCACAAGAAGGAGAAGAGCATGCCCTGGAACGTGGACACGCTTAG
CAAAGATGGCTTCAGCAAGAGCATGGTCAACACCAAGCCGGAGAAGACGGAGGAGGACTCAGAGGAGGTGAGGGAGCAGA
AACACAAGACCTTCGTGGAAAAGTGCGAGAAACAGACCAAGCACTTTGGCATGCTCGCCACTGGGATGACAGCCAAGAGT
ACCTGTCGGACAACGTCCACCTGGTGTGCGAGGAGACAGCCAATTACTTGGTCATCTGGTGCATTGATCTAGAGGTGGTG
GAGAAATGTGCACTCATGGAGCAGGTGGTCCCCCAGACAATCGTCATGCAGTTTATCCTGGAGCTGGCCAAGAGCCTGAA
GGTGGACCCCCGGGCCTGCTTCCGGCAGTTCTTCACTGAGATTAGGACAGCCGATCGCCAGTACGTGGAGGGCTTCAACG
ACGAGCTGGAAACCCTCAAAGAGCATGTGCAGGGCCGTGCCAAGCTGCCCATCAAGAAGGCCATGAAGGAGTACGAGGAG
GAGGAGCGCCAGAAGCAGCTTGGCCCTGGCGGCCTGGACCCCATCGAGGTCTACGAGTCCCTCCCCGAGGAACTCCAGAA
GTGCTTCCATGTGAAAGACGTGCAGATGCTGCAAGATGCCATCAGCAAGACGGACCCCACCAACGCGAAGTACCACATGC
AGCGCTGCTTTGACTCTGGCCTCTGGGTCCCCAACTCTAAGGCCAGCCAGGCCAAGGTGGGAGAGGAGGCGGGTCCCGGG
GACCCGCTGCTGGAAGCTGTTCCCAAGACGGGCAATGAGAAGGATGTCGGCGTG

Alignment

ORF - retro_hsap_3396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.51 %
• Parental protein coverage: 75.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EERSWEQKLEEMRKKEKSMPWNVDTLSKDGFSKSMVNTKPEKTEEDSEEVREQKHKTFVEKYEKQIKHFG
          E.RSWEQKLEEM.KKEKSMPWNVDTLSKDGFSKSMVNTKPEKTEEDSEEVREQKHKTFVEK.EKQ.KHFG
Retrocopy EDRSWEQKLEEMHKKEKSMPWNVDTLSKDGFSKSMVNTKPEKTEEDSEEVREQKHKTFVEKCEKQTKHFG

Parental  ML-RRWDDSQKYLSDNVHLVCEETANYLVIWCIDLEVEEKCALMEQVAHQTIVMQFILELAKSLKVDPRA
          ML.R.WDDSQ.YLSDNVHLVCEETANYLVIWCIDLEV.EKCALMEQV..QTIVMQFILELAKSLKVDPRA
Retrocopy ML<RHWDDSQEYLSDNVHLVCEETANYLVIWCIDLEVVEKCALMEQVVPQTIVMQFILELAKSLKVDPRA

Parental  CFRQFFTKIKTADRQYMEGFNDELEAFKERVRGRAKLRIEKAMKEYEEEERKKRLGPGGLDPVEVYESLP
          CFRQFFT.I.TADRQY.EGFNDELE..KE.V.GRAKL.I.KAMKEYEEEER.K.LGPGGLDP.EVYESLP
Retrocopy CFRQFFTEIRTADRQYVEGFNDELETLKEHVQGRAKLPIKKAMKEYEEEERQKQLGPGGLDPIEVYESLP

Parental  EELQKCFDVKDVQMLQDAISKMDPTDAKYHMQRCIDSGLWVPNSKASEAKEGEEAGPGDPLLEAVPKTGD
          EELQKCF.VKDVQMLQDAISK.DPT.AKYHMQRC.DSGLWVPNSKAS.AK.GEEAGPGDPLLEAVPKTG.
Retrocopy EELQKCFHVKDVQMLQDAISKTDPTNAKYHMQRCFDSGLWVPNSKASQAKVGEEAGPGDPLLEAVPKTGN

Parental  EKDVSV
          EKDV.V
Retrocopy EKDVGV

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	121.18 RPM
bodymap2_adrenal	0.02 RPM	112.87 RPM
bodymap2_brain	0.00 RPM	54.01 RPM
bodymap2_breast	0.00 RPM	84.34 RPM
bodymap2_colon	0.00 RPM	91.73 RPM
bodymap2_heart	0.00 RPM	50.07 RPM
bodymap2_kidney	0.00 RPM	64.98 RPM
bodymap2_liver	0.00 RPM	30.54 RPM
bodymap2_lung	0.00 RPM	106.52 RPM
bodymap2_lymph_node	0.00 RPM	81.99 RPM
bodymap2_ovary	0.00 RPM	76.70 RPM
bodymap2_prostate	0.00 RPM	86.86 RPM
bodymap2_skeletal_muscle	0.00 RPM	73.57 RPM
bodymap2_testis	0.00 RPM	73.96 RPM
bodymap2_thyroid	0.00 RPM	79.39 RPM
bodymap2_white_blood_cells	0.00 RPM	65.93 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3396 was not detected

EST

No EST(s) were mapped for retro_hsap_3396 retrocopy.

TSS

No TSS is located nearby retro_hsap_3396 retrocopy 5' end.

Lab

retro_hsap_3396 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3396 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2790
Macaca mulatta	retro_mmul_2113

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000105401	1 retrocopy	retro_hsap_3396 ,
Gorilla gorilla	ENSGGOG00000008098	1 retrocopy	retro_ggor_2299,
Macropus eugenii	ENSMEUG00000002278	1 retrocopy	retro_meug_1373,
Macaca mulatta	ENSMMUG00000003111	1 retrocopy	retro_mmul_2113,
Pongo abelii	ENSPPYG00000009551	1 retrocopy	retro_pabe_2790,
Ictidomys tridecemlineatus	ENSSTOG00000015962	1 retrocopy	retro_itri_328,

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	0.02 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.02 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	0.03 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).