RetrogeneDB ID: retro_hsap_4180

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:79585237..79585532(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000236604
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LYPLA2
• Ensembl ID: ENSG00000011009
• Aliases: LYPLA2, APT-2, DJ886K2.4
• Description: lysophospholipase II [Source:HGNC Symbol;Acc:6738]

Sequence

>retro_hsap_4180
CACAGCTGGGCTGAGCCCTGTCCACCATCCGGCTCCCTCATGTCAAGTACATCCATATCTGTCCCCTTGTGCCTAGGATC
CCTGTGACACTGAACATGAAGACGGTGATGCCCTCCTAGTTTGACCCAATGGGGCTGAGTCCAGGTGCCTCAGAGGACGA
GGCTGGCATCAAGAAGGCAGTAGAGAACTTAAGGTCCCAGCCTCTCCTCGGCCTCCTCCCTTCCCTGTCCCCCCAGGAAA
GCACTGGGCAGTGCCCCTGTCTGGCTCCCTTCCTGGGCCCCTTGGCAGCTTCCCC

Alignment

ORF - retro_hsap_4180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.05 %
• Parental protein coverage: 72.26 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HSWAD-ALSTIRLPHVKYI--CPHAPRIPVTLNMKMVMPSWFDLMGLSPDAPEDEAGIKKAAENRRG-PV
          HSWA..ALSTIRLPHVKYI..CP..PRIPVTLNMK.VMPS.FD.MGLSP.A.EDEAGIKKA.EN.R..P.
Retrocopy HSWAE<ALSTIRLPHVKYIHICPLVPRIPVTLNMKTVMPS*FDPMGLSPGASEDEAGIKKAVENLRS<PA

Parental  PLHGPHLPPPSGWHRGVELLAASAPGLPPGECP
          ....P..P.P.G.H..V..L..S.PG.P.G..P
Retrocopy SPRPPPFPVPPGKHWAVP-LSGSLPG-PLGSFP

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	23.56 RPM
bodymap2_adrenal	0.00 RPM	24.97 RPM
bodymap2_brain	0.00 RPM	6.94 RPM
bodymap2_breast	0.00 RPM	12.28 RPM
bodymap2_colon	0.00 RPM	17.44 RPM
bodymap2_heart	0.00 RPM	8.20 RPM
bodymap2_kidney	0.00 RPM	39.89 RPM
bodymap2_liver	0.00 RPM	26.97 RPM
bodymap2_lung	0.00 RPM	20.41 RPM
bodymap2_lymph_node	0.00 RPM	26.02 RPM
bodymap2_ovary	0.00 RPM	15.25 RPM
bodymap2_prostate	0.00 RPM	17.32 RPM
bodymap2_skeletal_muscle	0.00 RPM	14.26 RPM
bodymap2_testis	0.00 RPM	16.14 RPM
bodymap2_thyroid	0.00 RPM	19.90 RPM
bodymap2_white_blood_cells	0.00 RPM	34.20 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4180 was not detected

EST

No EST(s) were mapped for retro_hsap_4180 retrocopy.

TSS

No TSS is located nearby retro_hsap_4180 retrocopy 5' end.

Lab

retro_hsap_4180 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4180 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011625	1 retrocopy	retro_btau_1605,
Callithrix jacchus	ENSCJAG00000020914	1 retrocopy	retro_cjac_2585,
Dasypus novemcinctus	ENSDNOG00000011285	2 retrocopies	retro_dnov_1186, retro_dnov_134,
Homo sapiens	ENSG00000011009	3 retrocopies	retro_hsap_2023, retro_hsap_3577, retro_hsap_4180 ,
Homo sapiens	ENSG00000120992	3 retrocopies	retro_hsap_3078, retro_hsap_3485, retro_hsap_3897,
Macropus eugenii	ENSMEUG00000004768	2 retrocopies	retro_meug_1134, retro_meug_1526,
Nomascus leucogenys	ENSNLEG00000008646	1 retrocopy	retro_nleu_2958,
Otolemur garnettii	ENSOGAG00000032260	1 retrocopy	retro_ogar_2866,

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	0.00 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	0.00 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).