RetrogeneDB ID: retro_pabe_334

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:188984567..188985190(+)
• Located in intron of: ENSPPYG00000001478

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A1
• Ensembl ID: ENSPPYG00000029785
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; citrate transporter), member 1 [Source:HGNC Symbol;Acc:10979]

Sequence

>retro_pabe_334
ATGTTCGAGTTCCTCAGCAACCACATGCAGGATGCCCAGAGACAGCTGGACAGCAGGCACGAGCTGCTGTGTGGCCCAGG
AGCCAGCATGGCCAGTGCCGTGGTGGTCGTGTGCCCCATGAAGACCATCAAGGTGAAGTTCAACCACGACCAGACCTCCC
CGAACCCCAAGTAAACAGGATTCTCCCATGGGGTTAGGGAGATTGTGCGGGAATAAGGGCTGAAGGGAACGTACCAGGAC
CTCACGGCCACCATGCTGAAGCAGGGCTCGAACCAGGCTATCTGCTGCTTTGTCATGACCTCCCTGTGCAACTGGTACTG
AGAGGACAACCCCAACAAGCCCATGAACCTGCTGATCACTGGGGTCTTCGGAGCTATCGCAGGTGCAGCCAGTGTCTTTG
GAAACACTCCTCTGGACATGATTAAGACCCAGATGTAGGGCCTGGAGGTGCACAAATACTGGAACACATGAGACTGCGGC
TTGCAGATTCTGAGGAAGGAGGGGCTCAAGGCATTCTACAAAGGCACTGTCCCTGCCTGGGCTGGGTTGGCCTGTATGTG
GCCATAGTGTTTATCATGTATGATGAGGTGGTGAAGCTGCTCAGCAAAGTGTGGAAGACAGAC

Alignment

ORF - retro_pabe_334 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFEFLSNHMRDAQGRLDSTRGLLCGLGAGVAEAVVVVCPMETIKVKFIHDQTSPHPKYKGFFHGVREIVR
          MFEFLSNHM.DAQ..LDS...LLCG.GA..A.AVVVVCPM.TIKVKF.HDQTSP.PK..GF.HGVREIVR
Retrocopy MFEFLSNHMQDAQRQLDSRHELLCGPGASMASAVVVVCPMKTIKVKFNHDQTSPNPK*TGFSHGVREIVR

Parental  EQGLKGTYQGLTATVLKQGSNQAIRFFVMTSLRNWYRGDNPNKPMNPLITGVFGAIAGAASVFGNTPLDV
          E.GLKGTYQ.LTAT.LKQGSNQAI..FVMTSL.NWY..DNPNKPMN.LITGVFGAIAGAASVFGNTPLD.
Retrocopy E*GLKGTYQDLTATMLKQGSNQAICCFVMTSLCNWY*EDNPNKPMNLLITGVFGAIAGAASVFGNTPLDM

Parental  IKTRMQGLEAHKYRNTWDCGLQILRKEGLKAFYKGTVPR-LGRVCLDVAIVFIIYDEVVKLLNKVWKTD
          IKT.M.GLE.HKY.NT.DCGLQILRKEGLKAFYKGTVP..LG.V.L.VAIVFI.YDEVVKLL.KVWKTD
Retrocopy IKTQM*GLEVHKYWNT*DCGLQILRKEGLKAFYKGTVPA<LGWVGLYVAIVFIMYDEVVKLLSKVWKTD

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	16.70 RPM
SRP007412_cerebellum	0.12 RPM	10.58 RPM
SRP007412_heart	0.09 RPM	5.99 RPM
SRP007412_kidney	0.00 RPM	187.78 RPM
SRP007412_liver	0.03 RPM	61.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_334 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_334 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_334 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_485

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100075	2 retrocopies	retro_hsap_1632, retro_hsap_804,
Gorilla gorilla	ENSGGOG00000006198	2 retrocopies	retro_ggor_1230, retro_ggor_661,
Macaca mulatta	ENSMMUG00000005431	4 retrocopies	retro_mmul_1077, retro_mmul_1556, retro_mmul_1683, retro_mmul_485,
Nomascus leucogenys	ENSNLEG00000005215	2 retrocopies	retro_nleu_2866, retro_nleu_408,
Ochotona princeps	ENSOPRG00000011649	1 retrocopy	retro_opri_1053,
Pongo abelii	ENSPPYG00000029785	9 retrocopies	retro_pabe_1346, retro_pabe_1414, retro_pabe_1529, retro_pabe_1671, retro_pabe_3125, retro_pabe_3217, retro_pabe_334 , retro_pabe_3564, retro_pabe_719,
Pan troglodytes	ENSPTRG00000014057	3 retrocopies	retro_ptro_1139, retro_ptro_1364, retro_ptro_560,
Tursiops truncatus	ENSTTRG00000006845	1 retrocopy	retro_ttru_228,