RetrogeneDB ID: retro_hsap_3821

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:16904870..16905932(-)
• Located in intron of: ENSG00000173467

Retrocopy information

• Ensembl ID: ENSG00000232400
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAD17
• Ensembl ID: ENSG00000152942
• Aliases: RAD17, CCYC, HRAD17, R24L, RAD17SP, RAD24
• Description: RAD17 homolog (S. pombe) [Source:HGNC Symbol;Acc:9807]

Sequence

>retro_hsap_3821
ATGTCAAAAACTTTTCTTAGACCAAAGATATCTTCCACAAAGGTAACAGACTGGATTGACCCATCATTCAATGATTTTCT
AGAGTATAGAGACATCTCTACTATTACTGCCACATCATTAGGTGTGAATAACTCAAGTCATAGAGAAAAAAATGAGCCTT
CTACATTAGAAAGTAAGATATTTCCAGCTAGAAAAATAGGAAATCTGTCTTCCTTAGAACAGATATATGGTTTAGAAAAT
TCAAAAGACTATCTGTCTGAAAATGAACCATGGGTAGATAAATATAAACCAGAAAGTTAGCATGAACTTGGCTGTGCATG
AAAAGATAATTGAAGAAGTTGAAACCTGGTAAAAAGCTCAAGTCTTAGAAAGGCAACCAAAACAGGATGGATCTATTTTA
TTAATAACAGGTCCTCCTGGATGTGGAAAGACAACGACCAAAAAAACGCTATCAAAGGAGAATGGTATTCAAGTACAAGA
GTGGATTAATCCAGTTTTACCAGATTTCCAAAAAGATGATTTCAAGGAAATGTTTCATACTGAATCAAGCTTCCATATGT
TTCCCTATCAGTCTCAGATAGCAGTTTGCAAAGAGTTTCTACTAAGAGCAACAAAGTATAACAAGTTACAAATGCTTGGA
GATCATCTGAGAACTGATAAGAAGATAATTCTGGTTGAAGATTTACCTAACCAGTTTATAGGGATTCTCATACTTTACAT
GAAGTTCTAAGGAAGTATGTGAAGATTGGTCGATATCCTTTTATATTTATAATCTGTGACAGTCTCAGTGGTAAAAATAA
TCAAAGTTTCTTGTTCCCCAAAGAAATTCGGGAAGAGCATTCTACCTCAAATATTAGTTTCAACCCTGTGGCACCAACAA
TTACGATGAAATTTCTTAATCGAATAGTGACTATAGAGGCTAACAAGAATGGAGGAAAAATTACTGTCCCTGACAAAACT
TCTCTAGAGGTGCTCTGTCAAGGATGTTCTGGTGATATGAGAAGTGCAATAAACAGCCTCCAGATTTCTTCTTCAAAAGG
AGAAAACAACTTATGGCCAAGG

Alignment

ORF - retro_hsap_3821 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.92 %
• Parental protein coverage: 51.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKTFLRPKVSSTKVTDWVDPSFDDFLECSGVSTITATSLGVNNSSHRRKNGPSTLESSRFPARKRGNLS
          MSKTFLRPK.SSTKVTDW.DPSF.DFLE....STITATSLGVNNSSHR.KN.PSTLES..FPARK.GNLS
Retrocopy MSKTFLRPKISSTKVTDWIDPSFNDFLEYRDISTITATSLGVNNSSHREKNEPSTLESKIFPARKIGNLS

Parental  SLEQIYGLENSKEYLSENEPWVDKYKPETQHE-LAVHKKKIEEVETWLKAQVLERQPKQGGSILLITGPP
          SLEQIYGLENSK.YLSENEPWVDKYKPE..HE.LAVH.K.IEEVETW.KAQVLERQPKQ.GSILLITGPP
Retrocopy SLEQIYGLENSKDYLSENEPWVDKYKPES*HE>LAVHEKIIEEVETW*KAQVLERQPKQDGSILLITGPP

Parental  GCGKTTTLKILSKEHGIQVQEWINPVLPDFQKDDFKGMFNTESSFHMFPYQSQIAVFKEFLLRATKYNKL
          GCGKTTT.K.LSKE.GIQVQEWINPVLPDFQKDDFK.MF.TESSFHMFPYQSQIAV.KEFLLRATKYNKL
Retrocopy GCGKTTTKKTLSKENGIQVQEWINPVLPDFQKDDFKEMFHTESSFHMFPYQSQIAVCKEFLLRATKYNKL

Parental  QMLGDDLRTDKKIILVEDLPNQF-YRDSHTLHEVLRKYVRIGRCPLIFIISDSLSGDNNQRLLFPKEIQE
          QMLGD.LRTDKKIILVEDLPNQF.YRDSHTLHEVLRKYV.IGR.P.IFII.DSLSG.NNQ..LFPKEI.E
Retrocopy QMLGDHLRTDKKIILVEDLPNQF<YRDSHTLHEVLRKYVKIGRYPFIFIICDSLSGKNNQSFLFPKEIRE

Parental  ECSISNISFNPVAPTIMMKFLNRIVTIEANKNGGKITVPDKTSLELLCQGCSGDIRSAINSLQFSSSKGE
          E.S.SNISFNPVAPTI.MKFLNRIVTIEANKNGGKITVPDKTSLE.LCQGCSGD.RSAINSLQ.SSSKGE
Retrocopy EHSTSNISFNPVAPTITMKFLNRIVTIEANKNGGKITVPDKTSLEVLCQGCSGDMRSAINSLQISSSKGE

Parental  NNLRPR
          NNL.PR
Retrocopy NNLWPR

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	13.97 RPM
bodymap2_adrenal	0.00 RPM	27.57 RPM
bodymap2_brain	0.00 RPM	22.20 RPM
bodymap2_breast	0.04 RPM	23.97 RPM
bodymap2_colon	0.14 RPM	17.03 RPM
bodymap2_heart	0.00 RPM	25.62 RPM
bodymap2_kidney	0.00 RPM	41.86 RPM
bodymap2_liver	0.00 RPM	11.53 RPM
bodymap2_lung	0.00 RPM	11.87 RPM
bodymap2_lymph_node	0.00 RPM	23.79 RPM
bodymap2_ovary	0.00 RPM	29.99 RPM
bodymap2_prostate	0.07 RPM	28.46 RPM
bodymap2_skeletal_muscle	0.00 RPM	12.55 RPM
bodymap2_testis	0.00 RPM	68.85 RPM
bodymap2_thyroid	0.06 RPM	28.34 RPM
bodymap2_white_blood_cells	0.00 RPM	26.91 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3821 was not detected

EST

No EST(s) were mapped for retro_hsap_3821 retrocopy.

TSS

No TSS is located nearby retro_hsap_3821 retrocopy 5' end.

Lab

retro_hsap_3821 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3821 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1630

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000152942	1 retrocopy	retro_hsap_3821 ,
Macaca mulatta	ENSMMUG00000014881	1 retrocopy	retro_mmul_1630,
Nomascus leucogenys	ENSNLEG00000004118	1 retrocopy	retro_nleu_215,
Pan troglodytes	ENSPTRG00000016950	1 retrocopy	retro_ptro_2599,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 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	0.02 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).