RetrogeneDB ID: retro_hsap_3078

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:111866267..111866955(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000251483
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LYPLA1
• Ensembl ID: ENSG00000120992
• Aliases: LYPLA1, APT-1, APT1, LPL-I, LPL1, hAPT1
• Description: lysophospholipase I [Source:HGNC Symbol;Acc:6737]

Sequence

>retro_hsap_3078
ATGTGCAGCAATAACATGTCAGCCCCGCTGCCAGCCATCGTGCCCGCCACCTGGAAGGCCACCGCGGCGGTGATTTTCCT
TCATGGATTGGGAGATACTGGGCACCGATGGATAGAAGCCTTTGCAGGTATCAGAAGTTCACATATCAAATATATCTGCC
TGCATGCTCCTGTTATGCCTTTACATTAAATATGAACATGGCTGTGCCTTCATGGTTTGATATTATTGGGCTTTCACCAG
ATTCACAGGAGGACGAACCTGGGATTAAACAGGCAGCAGAAAATATAAAAGCTTTGATCGATCAAGAAGTGAAGAATGGC
ATTCCTTCTAACCGAATTATTGTAGGAGGATTTTCTCAGGGAGGAGCTTTATCTTTATATACTGCCCTTACCACGTAGCA
GAAACTGGCGGATGTCACTGCGCTCAGTTGCTGGCTTCCACTTCGGGCTTCATTTCCACAGGGTCCTATCAGGGGCGCTA
ACAGAGATATTTCTATTCTCCAGTGCCACGGAGATTGTGACCCGTTAGTTCCCCTGATGTTTGGTTCTCTTACGGTTGAA
AAACTAAAAACTTTGGCGATCCAGCCAATGTGACCTTTAAAACCTATGATGGTATGATACATAGCTCATGTCAACAGGAA
ATGATGGATGTCAAGCAATTCATTGATAAACTCCTACTTCCAATTGAT

Alignment

ORF - retro_hsap_3078 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.09 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MCGNNMSTPLPAIVPAARKATAAVIFLHGLGDTGHGWAEAFAGIRSSHIKYICPHAPVRPV-TLNMNVAM
          MC.NNMS.PLPAIVPA..KATAAVIFLHGLGDTGH.W.EAFAGIRSSHIKYIC.HAPV.P..TLNMN.A.
Retrocopy MCSNNMSAPLPAIVPATWKATAAVIFLHGLGDTGHRWIEAFAGIRSSHIKYICLHAPVMPL<TLNMNMAV

Parental  PSWFDIIGLSPDSQEDESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGALSLYTALTTQQKLAGV
          PSWFDIIGLSPDSQEDE.GIKQAAENIKALIDQEVKNGIPSNRII.GGFSQGGALSLYTALTT.QKLA.V
Retrocopy PSWFDIIGLSPDSQEDEPGIKQAAENIKALIDQEVKNGIPSNRIIVGGFSQGGALSLYTALTT*QKLADV

Parental  TALSCWLPLRASFPQGPIGGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLV-NPANVTFKTYEGMMH
          TALSCWLPLRASFPQGPI.GANRDISILQCHGDCDPLVPLMFGSLTVEKLKTL...PANVTFKTY.GM.H
Retrocopy TALSCWLPLRASFPQGPIRGANRDISILQCHGDCDPLVPLMFGSLTVEKLKTLA<DPANVTFKTYDGMIH

Parental  SSCQQEMMDVKQFIDKLLPPID
          SSCQQEMMDVKQFIDKLL.PID
Retrocopy SSCQQEMMDVKQFIDKLLLPID

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	40.79 RPM
bodymap2_adrenal	0.00 RPM	46.61 RPM
bodymap2_brain	0.00 RPM	16.88 RPM
bodymap2_breast	0.00 RPM	50.97 RPM
bodymap2_colon	0.00 RPM	44.38 RPM
bodymap2_heart	0.00 RPM	68.12 RPM
bodymap2_kidney	0.00 RPM	110.52 RPM
bodymap2_liver	0.00 RPM	66.54 RPM
bodymap2_lung	0.00 RPM	48.10 RPM
bodymap2_lymph_node	0.00 RPM	54.00 RPM
bodymap2_ovary	0.00 RPM	33.73 RPM
bodymap2_prostate	0.00 RPM	66.56 RPM
bodymap2_skeletal_muscle	0.00 RPM	44.81 RPM
bodymap2_testis	0.00 RPM	116.87 RPM
bodymap2_thyroid	0.00 RPM	46.31 RPM
bodymap2_white_blood_cells	0.00 RPM	102.18 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3078 was not detected

EST

No EST(s) were mapped for retro_hsap_3078 retrocopy.

TSS

No TSS is located nearby retro_hsap_3078 retrocopy 5' end.

Lab

retro_hsap_3078 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3078 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2114
Pongo abelii	retro_pabe_2550

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006978	1 retrocopy	retro_cfam_523,
Callithrix jacchus	ENSCJAG00000011562	2 retrocopies	retro_cjac_1260, retro_cjac_3100,
Cavia porcellus	ENSCPOG00000022715	3 retrocopies	retro_cpor_142, retro_cpor_549, retro_cpor_782,
Dipodomys ordii	ENSDORG00000001479	1 retrocopy	retro_dord_88,
Equus caballus	ENSECAG00000016530	1 retrocopy	retro_ecab_238,
Echinops telfairi	ENSETEG00000001727	2 retrocopies	retro_etel_612, retro_etel_791,
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,
Myotis lucifugus	ENSMLUG00000008208	1 retrocopy	retro_mluc_1683,
Macaca mulatta	ENSMMUG00000013157	3 retrocopies	retro_mmul_1734, retro_mmul_2459, retro_mmul_2474,
Nomascus leucogenys	ENSNLEG00000001027	4 retrocopies	retro_nleu_1137, retro_nleu_2015, retro_nleu_2817, retro_nleu_2869,
Oryctolagus cuniculus	ENSOCUG00000006751	3 retrocopies	retro_ocun_1510, retro_ocun_1623, retro_ocun_1679,
Pteropus vampyrus	ENSPVAG00000005246	2 retrocopies	retro_pvam_224, retro_pvam_838,
Rattus norvegicus	ENSRNOG00000008320	3 retrocopies	retro_rnor_1747, retro_rnor_2612, retro_rnor_406,
Tarsius syrichta	ENSTSYG00000012350	6 retrocopies	retro_tsyr_1287, retro_tsyr_1303, retro_tsyr_1465, retro_tsyr_1901, retro_tsyr_1996, retro_tsyr_2158,
Tursiops truncatus	ENSTTRG00000011836	3 retrocopies	retro_ttru_1643, retro_ttru_169, retro_ttru_291,