RetrogeneDB ID: retro_pabe_142

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:33356308..33357001(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000016496
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LYPLA2
• Ensembl ID: ENSPPYG00000001733
• Aliases: None
• Description: lysophospholipase II [Source:HGNC Symbol;Acc:6738]

Sequence

>retro_pabe_142
ATGTGTGGTAACACCATGTCTGTGCCTCTGCTCACCGATGCTGCCACCGTGTCTGGAGCTGAGCGGGAAACGGCCGTGGT
TATTTTTTTACATGGACTTGGAGACACAGGGCACAGCTGGGCTTACGCCCTCTCCACCATCCGGCTCCCTCATGTCAAGT
ACATCTGTCCCCATGTGCCTAGGATCCCTGTGACCCTCAACATGAAGATGGTGATGCCCTCCTGGTTTGACCTGATGGGG
CTGGGTCCAGATGCCCCAGAGGACGAGGCTGGCATCAAAAAGGCAGCAGAGAACATCAAGGCCTTGATTGAGCATGAAAT
GAAGAATGGGATCCCTGCCAATCGAATCATCCTGGGAGGCTTTTCACAGGGCGGGGCCCTGTCCCTCTACACGGCCCTCA
CCTGCCCCCACCCTCTGGCTGGCATCGTGGTGTTGAGCTGCGGGCTGCCTCTGCACCGGGCCTTACCCCAGGCAGCTAAT
GGCAGTGCCAAGGACCTGGCCATCCTCCAGTGCCATGGGGAGCTGGACCCCATGGTGCCTGTACGGTTTGGGGCTCTGAC
GGCTGAGAAGCTCCGGTCTGTTGTCATACCTGCCAGGGTCCAGTTCAAGACATACCCGGGTGTCATGCACAGCTCCTGTC
CTCAGGAGATGGCAGCTGTGAAGGAATTTCTTGAGAAGCTGCTGCCTCCTGTC

Alignment

ORF - retro_pabe_142 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SWADALSTIRLPHVKYICPHAPRIPVTLNMKMVMPSWFDLMGLSPDAPEDEAGIKKAAENIKALIEHEMK
          SWA.ALSTIRLPHVKYICPH.PRIPVTLNMKMVMPSWFDLMGL.PDAPEDEAGIKKAAENIKALIEHEMK
Retrocopy SWAYALSTIRLPHVKYICPHVPRIPVTLNMKMVMPSWFDLMGLGPDAPEDEAGIKKAAENIKALIEHEMK

Parental  NGIPANRIVLGGFSQGGALSLYTALTCPHPLAGIVALSCWLPLHRAFPQAANGSA-DLAILQC-GELDPM
          NGIPANRI.LGGFSQGGALSLYTALTCPHPLAGIV.LSC.LPLHRA.PQAANGSA.DLAILQC.GELDPM
Retrocopy NGIPANRIILGGFSQGGALSLYTALTCPHPLAGIVVLSCGLPLHRALPQAANGSAKDLAILQCHGELDPM

Parental  VPVRFGA-TAEKLRSVVTPARVQFKTYPGVMHSSCPQEMAAVKEFLEKLLPPV
          VPVRFGA.TAEKLRSVV.PARVQFKTYPGVMHSSCPQEMAAVKEFLEKLLPPV
Retrocopy VPVRFGALTAEKLRSVVIPARVQFKTYPGVMHSSCPQEMAAVKEFLEKLLPPV

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
SRP007412_brain_prefrontal_cortex	1.49 RPM	0.00 RPM
SRP007412_cerebellum	1.09 RPM	0.00 RPM
SRP007412_heart	0.72 RPM	0.00 RPM
SRP007412_kidney	4.31 RPM	0.00 RPM
SRP007412_liver	2.14 RPM	0.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_142 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_142 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_142 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3577
Gorilla gorilla	retro_ggor_2413

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 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,
Gorilla gorilla	ENSGGOG00000004330	3 retrocopies	retro_ggor_2114, retro_ggor_2413, retro_ggor_2626,
Macropus eugenii	ENSMEUG00000004768	2 retrocopies	retro_meug_1134, retro_meug_1526,
Microcebus murinus	ENSMICG00000005841	1 retrocopy	retro_mmur_1166,
Otolemur garnettii	ENSOGAG00000032260	1 retrocopy	retro_ogar_2866,
Pongo abelii	ENSPPYG00000001733	1 retrocopy	retro_pabe_142 ,
Pongo abelii	ENSPPYG00000018590	3 retrocopies	retro_pabe_2550, retro_pabe_3177, retro_pabe_3565,
Tursiops truncatus	ENSTTRG00000016127	1 retrocopy	retro_ttru_1522,