RetrogeneDB ID: retro_pabe_2765

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:109615276..109615595(-)
• Located in intron of: ENSPPYG00000015672

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: LSM2
• Ensembl ID: ENSPPYG00000016461
• Aliases: None
• Description: LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:13940]

Sequence

>retro_pabe_2765
CCTCTTTCTGGTCCAGCCCACAGCACCAGCACCATGCTCTTCTATTATTTTTTTCAAGTCCCTTGTGGGCAAGCATGTGG
TCGTGGAACTCAAGAATGACCTGAGCATCTGTGGAACCCTCCACTCTGTGGATCAGTATCTCAACATCAAACTAACTAAT
ATCAGTGTCATAGACCCTGAGAAATATCCTCACATGTTATCAGTGAAGAACTGCTTCATTCAGGGTTCAGTGGTCCGATA
CATGCAGTTGCCAGCAGACGAGGTCCACGAACAGTTGCTACAGGATGCAGCAAGGAAGGAACCCCTGCAGTAGAAACAG

Alignment

ORF - retro_pabe_2765 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.18 %
• Parental protein coverage: 60.23 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PVRPAARGASTMLFYSFF-KSLVGKDVVVELKNDLSICGTLHSVDQYLNIKLTDISVTDPEKYPHMLSVK
          P....A...STMLFY.FF.KSLVGK.VVVELKNDLSICGTLHSVDQYLNIKLT.ISV.DPEKYPHMLSVK
Retrocopy PLSGPAHSTSTMLFYYFF>KSLVGKHVVVELKNDLSICGTLHSVDQYLNIKLTNISVIDPEKYPHMLSVK

Parental  NCFIRGSVVRYVQLPADEVDTQLLQDAARKEALQQKQ
          NCFI.GSVVRY.QLPADEV..QLLQDAARKE.LQ.KQ
Retrocopy NCFIQGSVVRYMQLPADEVHEQLLQDAARKEPLQ*KQ

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	0.00 RPM	11.28 RPM
SRP007412_cerebellum	0.12 RPM	19.70 RPM
SRP007412_heart	0.00 RPM	8.52 RPM
SRP007412_kidney	0.03 RPM	10.74 RPM
SRP007412_liver	0.00 RPM	8.78 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2765 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2765 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2765 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3361
Pan troglodytes	retro_ptro_2284
Macaca mulatta	retro_mmul_2099
Callithrix jacchus	retro_cjac_1828

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002601	2 retrocopies	retro_cjac_1828, retro_cjac_2088,
Felis catus	ENSFCAG00000004511	1 retrocopy	retro_fcat_309,
Macaca mulatta	ENSMMUG00000006832	3 retrocopies	retro_mmul_1389, retro_mmul_1875, retro_mmul_2099,
Mus musculus	ENSMUSG00000007050	1 retrocopy	retro_mmus_931,
Nomascus leucogenys	ENSNLEG00000006371	1 retrocopy	retro_nleu_960,
Ochotona princeps	ENSOPRG00000003668	2 retrocopies	retro_opri_250, retro_opri_917,
Pongo abelii	ENSPPYG00000016461	1 retrocopy	retro_pabe_2765 ,
Pan troglodytes	ENSPTRG00000017986	3 retrocopies	retro_ptro_1349, retro_ptro_2063, retro_ptro_2284,
Rattus norvegicus	ENSRNOG00000048725	1 retrocopy	retro_rnor_1463,
Ictidomys tridecemlineatus	ENSSTOG00000013144	1 retrocopy	retro_itri_189,