RetrogeneDB ID: retro_hsap_3275

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 5:177592702..177593553(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000251211
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: APOA1BP
• Ensembl ID: ENSG00000163382
• Aliases: APOA1BP, AIBP, YJEFN1
• Description: apolipoprotein A-I binding protein [Source:HGNC Symbol;Acc:18453]

Sequence

>retro_hsap_3275
ATGTCCGGCCTGCGGGCGCTGCCGGGGCTCAGGCTGCTGGTTGCGGCTCGCGCCTGCGCGAATCAAAAGCCAGACCAGCG
CCTGCCGCTCGGGACCCACCTCGTGGGGACGGCAGCGGCTGAACTCGGGTGGCCGCTGGGACTCAGCGGTCATGGCGAGC
ATAGCGGTGAAGCACCTGAGCCAGGAGGAAGCCCAGGTCGTGGACCAGGAGCTATTCAACGAGTACTAGTTCAGCGTGGC
CCGACTTGTGGAGCTGGCCGGGCTGAGCTGCGCCGCAGCCATCGCCAAGGCATATTCCCCCACGTCCATGTCCAGGAGCT
CCCCTACTGTCCTGGTCATCTGTGGCCCGGGGAATAATGGAGGAGATGGTCTGGTCTGTGCTGCGCACCTCAAACTCTTT
GGCTAACCGGCCAACCATCTATTACCCCAAAAGGCCCAACCAGCCCCTCTTCATTGCGTTGGTGACCCCGTGTCAGAAAA
TGGACATCCCTTTCCTTGGGGAAATGCGCTCAGAGCCCGTGATGATTGAGCTGTATGAGCTGGTGGTGGATGCCATCTTC
GGCTTCAGCTTCGAGGGTGATGTTCGGGAACGTTCCACAGCATCCTGAGTGTCCTGAAGGGATTCACCGTGCCCACTGCC
GGCATCAACATTCCCTCTGGATGGGATGTGGAGAAGGGAAACTCTGGAGGGATCCAGCCAGACTTGCTCATCTCCCTCAC
AGCACCCAAAAAGTCTGCAACCCAGGTTACCCGGTCGCCACCATTACCTGGGGGGTCGTTTTGTGCCACCTGCTCTGGAA
AAGAAGTAGCACCTGAACCTGCCCCTACCCTGACACCAAGTGTGTGTATGG

Alignment

ORF - retro_hsap_3275 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.38 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSRLRALLGLGLLVA-GSRV-PRIKSQTIACRSGPTWWGPQRLNSGGRWDSEVMASTVVKYLSQEEAQAV
          MS.LRAL.GL.LLVA.GSR...RIKSQT.ACRSGPT.WG.QRLNSGGRWDS.VMAS..VK.LSQEEAQ.V
Retrocopy MSGLRALPGLRLLVA<GSRL<ARIKSQTSACRSGPTSWGRQRLNSGGRWDSAVMASIAVKHLSQEEAQVV

Parental  DQELFNEYQFSVDQLMELAGLSCATAIAKAYPPTSMSRSPPTVLVICGPGNNGGDGLVCARHLKLFG-YE
          DQELFNEY.FSV..L.ELAGLSCA.AIAKAY.PTSMSRS.PTVLVICGPGNNGGDGLVCA.HLKLFG...
Retrocopy DQELFNEY*FSVARLVELAGLSCAAAIAKAYSPTSMSRSSPTVLVICGPGNNGGDGLVCAAHLKLFG>NR

Parental  PTIYYPKRPNKPLFTALVTQCQKMDIPFLGEMPAEPMTIDELYELVVDAIFGFSFKGDVRE-PFHSILSV
          PTIYYPKRPN.PLF.ALVT.CQKMDIPFLGEM..EP..I.ELYELVVDAIFGFSF.GDVRE..FHSILSV
Retrocopy PTIYYPKRPNQPLFIALVTPCQKMDIPFLGEMRSEPVMI-ELYELVVDAIFGFSFEGDVRE<TFHSILSV

Parental  LKGLTVPIASIDIPSGWDVEKGNAGGIQPDLLISLTAPKKSATQFT-GRYHYLGGRFVPPALEKKYQLNL
          LKG.TVP.A.I.IPSGWDVEKGN.GGIQPDLLISLTAPKKSATQ.T.GR.HYLGGRFVPPALEKK..LNL
Retrocopy LKGFTVPTAGINIPSGWDVEKGNSGGIQPDLLISLTAPKKSATQVT>GRHHYLGGRFVPPALEKK*HLNL

Parental  PPYPDTECVY
          P......CV.
Retrocopy PLP*HQVCVW

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	27.81 RPM
bodymap2_adrenal	0.02 RPM	48.53 RPM
bodymap2_brain	0.00 RPM	26.18 RPM
bodymap2_breast	0.00 RPM	42.10 RPM
bodymap2_colon	0.06 RPM	34.92 RPM
bodymap2_heart	0.02 RPM	34.89 RPM
bodymap2_kidney	0.12 RPM	55.53 RPM
bodymap2_liver	0.02 RPM	29.83 RPM
bodymap2_lung	0.00 RPM	27.34 RPM
bodymap2_lymph_node	0.00 RPM	35.60 RPM
bodymap2_ovary	0.00 RPM	42.33 RPM
bodymap2_prostate	0.00 RPM	43.47 RPM
bodymap2_skeletal_muscle	0.00 RPM	25.72 RPM
bodymap2_testis	0.02 RPM	39.57 RPM
bodymap2_thyroid	0.02 RPM	41.52 RPM
bodymap2_white_blood_cells	0.00 RPM	24.81 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3275 was not detected

EST

No EST(s) were mapped for retro_hsap_3275 retrocopy.

TSS

No TSS is located nearby retro_hsap_3275 retrocopy 5' end.

Lab

retro_hsap_3275 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3275 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2215
Gorilla gorilla	retro_ggor_2228
Pongo abelii	retro_pabe_2709
Macaca mulatta	retro_mmul_2060

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000163382	2 retrocopies	retro_hsap_1973, retro_hsap_3275 ,
Gorilla gorilla	ENSGGOG00000000754	1 retrocopy	retro_ggor_2228,
Macaca mulatta	ENSMMUG00000002623	2 retrocopies	retro_mmul_1364, retro_mmul_2060,
Nomascus leucogenys	ENSNLEG00000012663	2 retrocopies	retro_nleu_2615, retro_nleu_2992,
Pongo abelii	ENSPPYG00000000713	2 retrocopies	retro_pabe_1692, retro_pabe_2709,
Pan troglodytes	ENSPTRG00000001463	2 retrocopies	retro_ptro_1315, retro_ptro_2215,

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	0.04 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	0.03 RPM
GBR_HG00133	0.00 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.03 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.03 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	0.02 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).