RetrogeneDB ID: retro_pabe_1994

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2a:51412645..51412884(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM6
• Ensembl ID: ENSPPYG00000015105
• Aliases: None
• Description: LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17017]

Sequence

>retro_pabe_1994
ATGAACCTTTGGAAGCAAACCTCCAGTGCCTTCTTAAAGCATATCATCAGAAGACCAGTTGTGGTAAAATTAAATCCTAG
AGTGAATTATTGAGGGGACCTGGCTTGCCTGGATGACTGCTCGAATATAGCCCTGAGACGGCAGAGGAATATATAAGTGG
ACAACCAAAGATTAAGTATGGGTATGCATTTGTCTGAGGAAACAATGTGTCGCACATCAGTACACAGGAGAGAAGGATG

Alignment

ORF - retro_pabe_1994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLRKQTPSDFLKQIIGRPVVVKLNSGVDYRGVLACLDGYMNIAL-EQTEEYVNGQLKNKYGDAFIRGNN
          M.L.KQT.S.FLK.II.RPVVVKLN..V.Y.G.LACLD...NIAL.E..EEY..GQ.K.KYG.AF..GNN
Retrocopy MNLWKQTSSAFLKHIIRRPVVVKLNPRVNY*GDLACLDDCSNIAL<ETAEEYISGQPKIKYGYAFV*GNN

Parental  VLYISTQKRRM
          V..ISTQ.RRM
Retrocopy VSHISTQERRM

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	6.25 RPM
SRP007412_cerebellum	0.00 RPM	6.93 RPM
SRP007412_heart	0.00 RPM	4.40 RPM
SRP007412_kidney	0.00 RPM	6.03 RPM
SRP007412_liver	0.00 RPM	5.75 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1994 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1994 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1994 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2107
Pan troglodytes	retro_ptro_1545
Gorilla gorilla	retro_ggor_1638
Macaca mulatta	retro_mmul_991

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002482	4 retrocopies	retro_cjac_1173, retro_cjac_1278, retro_cjac_3176, retro_cjac_3248,
Dasypus novemcinctus	ENSDNOG00000009322	5 retrocopies	retro_dnov_1118, retro_dnov_176, retro_dnov_2092, retro_dnov_301, retro_dnov_664,
Microcebus murinus	ENSMICG00000000571	1 retrocopy	retro_mmur_1563,
Macaca mulatta	ENSMMUG00000005524	2 retrocopies	retro_mmul_668, retro_mmul_991,
Mus musculus	ENSMUSG00000031683	2 retrocopies	retro_mmus_820, retro_mmus_956,
Otolemur garnettii	ENSOGAG00000026665	1 retrocopy	retro_ogar_233,
Pongo abelii	ENSPPYG00000004847	2 retrocopies	retro_pabe_381, retro_pabe_489,
Pongo abelii	ENSPPYG00000015105	1 retrocopy	retro_pabe_1994 ,
Pan troglodytes	ENSPTRG00000016488	1 retrocopy	retro_ptro_1545,
Tarsius syrichta	ENSTSYG00000012759	4 retrocopies	retro_tsyr_1332, retro_tsyr_1727, retro_tsyr_340, retro_tsyr_653,