RetrogeneDB ID: retro_hsap_3271

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:175735098..175735618(+)
• Located in intron of: ENSG00000170085

Retrocopy information

• Ensembl ID: ENSG00000251667
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BRCC3
• Ensembl ID: ENSG00000185515
• Aliases: BRCC3, BRCC36, C6.1A, CXorf53
• Description: BRCA1/BRCA2-containing complex, subunit 3 [Source:HGNC Symbol;Acc:24185]

Sequence

>retro_hsap_3271
GTTCATCTAGAGTCTGACACTTTCCTTGTTTGTCTCAACCATGCTCTGAGCACAGAGAAGGAGGAAGTGATGGGGCTGTG
GATAGGGGAGTTGAACAATGATACAAGGAGTGACTCCAAATTTGCATATACTGGAACTGAAATGCGCACAGTTGCTGAAA
AGGTTGATGCCATCAGAATTGTTCACATTCGTTCTGTCATCATCTTAACGACGTTCTGATAAGAGGAAGGACCAAGTAGA
AATTTCACCAGGGCAGCTGTCTGCAGCTTCAACAGAGGCAGAGAAGTTGGCTGAACTGACAGGCCACCCCATGAGAGTTG
TGGGCTGGTATCATTCCCATCCTCATATAACTGTTTGGCCTTCACATGTTGATGTTCGCACCCAAGCCATGTACCAGATG
ATGGATCAAGGCTTTGTAGGACTTATTTTTTCCTGTTTCATAGAAGATAAGAACACAAGGGCTGGCCGGGTACTCTACAC
TTGCTTCCAATCCATACAGGCCCAAAAGAGTTCAGAGTCC

Alignment

ORF - retro_hsap_3271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.1 %
• Parental protein coverage: 54.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VHLESDAFLVCLNHALSTEKEEVMGLCIGELNDDTRSDSKFAYTGTEMRTVAEKVDAVRIVHIHSVIIL-
          VHLESD.FLVCLNHALSTEKEEVMGL.IGELN.DTRSDSKFAYTGTEMRTVAEKVDA.RIVHI.SVIIL.
Retrocopy VHLESDTFLVCLNHALSTEKEEVMGLWIGELNNDTRSDSKFAYTGTEMRTVAEKVDAIRIVHIRSVIIL>

Parental  RRSDKRKDRVEISPEQLSAASTEAERLAELTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFV
          RRSDKRKD.VEISP.QLSAASTEAE.LAELTG.PMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFV
Retrocopy RRSDKRKDQVEISPGQLSAASTEAEKLAELTGHPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFV

Parental  GLIFSCFIEDKNTKTGRVLYTCFQSIQAQKSSES
          GLIFSCFIEDKNT..GRVLYTCFQSIQAQKSSES
Retrocopy GLIFSCFIEDKNTRAGRVLYTCFQSIQAQKSSES

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	0.26 RPM	13.87 RPM
bodymap2_adrenal	0.08 RPM	16.31 RPM
bodymap2_brain	0.07 RPM	15.12 RPM
bodymap2_breast	0.10 RPM	17.45 RPM
bodymap2_colon	0.00 RPM	20.88 RPM
bodymap2_heart	0.02 RPM	18.07 RPM
bodymap2_kidney	0.08 RPM	29.41 RPM
bodymap2_liver	0.02 RPM	13.41 RPM
bodymap2_lung	0.00 RPM	6.36 RPM
bodymap2_lymph_node	0.27 RPM	12.13 RPM
bodymap2_ovary	0.39 RPM	18.79 RPM
bodymap2_prostate	0.16 RPM	21.91 RPM
bodymap2_skeletal_muscle	0.00 RPM	13.51 RPM
bodymap2_testis	0.40 RPM	10.92 RPM
bodymap2_thyroid	0.04 RPM	25.06 RPM
bodymap2_white_blood_cells	0.00 RPM	30.65 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3271 was not detected

EST

No EST(s) were mapped for retro_hsap_3271 retrocopy.

TSS

No TSS is located nearby retro_hsap_3271 retrocopy 5' end.

Lab

retro_hsap_3271 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3271 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007817	2 retrocopies	retro_btau_1327, retro_btau_1646,
Cavia porcellus	ENSCPOG00000001882	2 retrocopies	retro_cpor_388, retro_cpor_627,
Homo sapiens	ENSG00000185515	1 retrocopy	retro_hsap_3271 ,
Gorilla gorilla	ENSGGOG00000027248	1 retrocopy	retro_ggor_2226,
Monodelphis domestica	ENSMODG00000016487	1 retrocopy	retro_mdom_930,
Mus musculus	ENSMUSG00000031201	1 retrocopy	retro_mmus_672,
Nomascus leucogenys	ENSNLEG00000014460	1 retrocopy	retro_nleu_2940,
Sarcophilus harrisii	ENSSHAG00000005392	1 retrocopy	retro_shar_51,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.03 RPM
CEU_NA11930	0.20 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.07 RPM
CEU_NA12751	0.02 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.14 RPM
CEU_NA12873	0.13 RPM
FIN_HG00183	0.11 RPM
FIN_HG00277	0.04 RPM
FIN_HG00315	0.03 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.02 RPM
FIN_HG00338	0.06 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.08 RPM
FIN_HG00378	0.04 RPM
GBR_HG00099	0.03 RPM
GBR_HG00111	0.09 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.10 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.07 RPM
GBR_HG00134	0.09 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.14 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.06 RPM
TSI_NA20513	0.05 RPM
TSI_NA20518	0.11 RPM
TSI_NA20532	0.34 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.03 RPM
TSI_NA20765	0.12 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.03 RPM
TSI_NA20798	0.06 RPM
YRI_NA18870	0.17 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.11 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.14 RPM
YRI_NA19214	0.02 RPM
YRI_NA19223	0.12 RPM

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Indel association:

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