RetrogeneDB ID: retro_pabe_3333

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:56252698..56253235(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC11A
• Ensembl ID: ENSPPYG00000006881
• Aliases: None
• Description: Signal peptidase complex catalytic subunit SEC11A [Source:UniProtKB/Swiss-Prot;Acc:Q5R9C7]

Sequence

>retro_pabe_3333
ATGCTGTCTCTAGACTTTTTGGATGATGTGCAGTGGATGAACAAGCGGCAGCTCTATTATCAAGTCCTAAATTTTGGAAT
GATTGTCTCATCAGCACTCATGATCTGGAAGGGGTTACTGGTAATAACTGGAAGTGAAAGTCCAATTGTAGTGTTGCTCA
GTGGCAGCATGGAACCTGCATTTCATAGAGGATATCTTCTCTTTCTAACGATTCGAGTTGAAGATCCCATATGAGTGGGA
GAAATTGCTGTTCTAAGGATAGAAGGAAGAAAGATTCCTATAGTTCACCGAATCTTGAAGGTTCATGAAAAGCAAAATGG
GCATATCAAGTTTTTGACCCAAGGAGATAATAATGCGGTTGATGACCGAGGCCTCTATAAACAAGAACAACATTGGCTAG
AGAAAAAAGATGTCGTGGGGAGAGCCAGGGGATTTGTTCCTTATATTGGAATTGGGACGAGCCTCATGAATGACTATCCT
AAATTTAAGTATGAAGTGCTCTTTTTGCTGGGTTTATTTGTGCTGGTCCATCGTGAG

Alignment

ORF - retro_pabe_3333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.5 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLSLDFLDDVRRMNKRQLYYQVLNFGMIVSSALMIWKGLMVITGSESPIVVVLSGSMEPAFHRGDLLFLT
          MLSLDFLDDV..MNKRQLYYQVLNFGMIVSSALMIWKGL.VITGSESPIVV.LSGSMEPAFHRG.LLFLT
Retrocopy MLSLDFLDDVQWMNKRQLYYQVLNFGMIVSSALMIWKGLLVITGSESPIVVLLSGSMEPAFHRGYLLFLT

Parental  NRVEDPIRVGEIVVFRIEGREIPIVHRVLKIHEKQNGHIKFLTKGDNNAVDDRGLYKQGQHWLEKKDVVG
          .RVEDPI.VGEI.V.RIEGR.IPIVHR.LK.HEKQNGHIKFLT.GDNNAVDDRGLYKQ.QHWLEKKDVVG
Retrocopy IRVEDPI*VGEIAVLRIEGRKIPIVHRILKVHEKQNGHIKFLTQGDNNAVDDRGLYKQEQHWLEKKDVVG

Parental  RARGFVPYIGIVTILMNDYPKFKYAVLFLLGLFVLVHRE
          RARGFVPYIGI.T.LMNDYPKFKY.VLFLLGLFVLVHRE
Retrocopy RARGFVPYIGIGTSLMNDYPKFKYEVLFLLGLFVLVHRE

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	19.13 RPM
SRP007412_cerebellum	0.00 RPM	17.02 RPM
SRP007412_heart	0.00 RPM	32.69 RPM
SRP007412_kidney	0.00 RPM	80.51 RPM
SRP007412_liver	0.03 RPM	49.18 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3333 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3333 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4058
Pan troglodytes	retro_ptro_2751
Gorilla gorilla	retro_ggor_2726
Macaca mulatta	retro_mmul_2343

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012889	1 retrocopy	retro_cfam_1416,
Callithrix jacchus	ENSCJAG00000016146	1 retrocopy	retro_cjac_1496,
Felis catus	ENSFCAG00000029786	2 retrocopies	retro_fcat_1178, retro_fcat_1908,
Homo sapiens	ENSG00000140612	1 retrocopy	retro_hsap_4058,
Gorilla gorilla	ENSGGOG00000011129	1 retrocopy	retro_ggor_2726,
Monodelphis domestica	ENSMODG00000019364	1 retrocopy	retro_mdom_726,
Pongo abelii	ENSPPYG00000006881	1 retrocopy	retro_pabe_3333 ,
Pan troglodytes	ENSPTRG00000007404	1 retrocopy	retro_ptro_2751,
Tupaia belangeri	ENSTBEG00000012320	3 retrocopies	retro_tbel_1139, retro_tbel_2280, retro_tbel_745,
Tursiops truncatus	ENSTTRG00000005833	1 retrocopy	retro_ttru_1237,