RetrogeneDB ID: retro_pabe_1346

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:30613216..30613729(+)
• Located in intron of: None

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_1346
GAGTTCCTCGGCACCCAGATGCGGGATGCCCAGGGACTGCTAAACAGCAGGCGCGGGCTGCTGTGCGGCCTGGGCGCCGG
CGTGGCCGAGGCCGTGGTGGTTGTCCCTCCCATGGAGACCATCAAAGTGAAGTTCATCCACGACCAGACCTCCCCAAACC
CAAGAACAGAGAATTCTTTGGGGTTAGGGAGATTGTGCGGGAACAAGAGCTGAGGGGATTTACCAGGGCCTCACGGCCTC
CACGCTGAAGCAGGGCTGGAACCAGGCCATTGCTTCTTCGTCCTGACCTCCCCGCAGCAACTGATACCAAAGGGACAAAC
CCATGAACCCGCTGATCATTGGGGTCTTCTGAGCCATTGTGGGCGCAGACAGCGTCTTCGGAAACGCCCCTCTGGACAGG
ATCGAGACCCGGATGCGGGGCGTGGAAGTGCACAAACACCGGAACAGTGGAATGCAGCTGCAGATCCCGAGGAAGGAGGG
GCTCAATGCCTTCACAAGGGCACTGCCCCCCGC

Alignment

ORF - retro_pabe_1346 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.88 %
• Parental protein coverage: 85.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EFLSNHMRDAQGRLDSTRGLLCGLGAGVAEAVVVVCPMETIKVKFIHDQTSPH-PKYKGFFHGVREIVRE
          EFL...MRDAQG.L.S.RGLLCGLGAGVAEAVVVV.PMETIKVKFIHDQTSP..PK...FF.GVREIVRE
Retrocopy EFLGTQMRDAQGLLNSRRGLLCGLGAGVAEAVVVVPPMETIKVKFIHDQTSPN<PKNREFF-GVREIVRE

Parental  QGLK-GTYQGLTATVLKQGSNQAIR-FFVMTSLR-NWYRGDNPNKPMNPLITGVFGAIAGAASVFGNTPL
          Q.L..G.YQGLTA..LKQG.NQAI..FFV.TS...N.Y..D...KPMNPLI.GVF.AI.GA.SVFGN.PL
Retrocopy QELR<GIYQGLTASTLKQGWNQAIA<FFVLTSPQ>N*YQRD---KPMNPLIIGVF*AIVGADSVFGNAPL

Parental  DVIKTRMQGLEAHKYRNTWDCGLQILRKEGLKAF-YKGTVPR
          D.I.TRM.G.E.HK.RN.....LQI.RKEGL.AF..KGT.PR
Retrocopy DRIETRMRGVEVHKHRNS-GMQLQIPRKEGLNAF<HKGTAPR

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	0.00 RPM	10.58 RPM
SRP007412_heart	0.00 RPM	5.99 RPM
SRP007412_kidney	0.00 RPM	187.78 RPM
SRP007412_liver	0.00 RPM	61.54 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1346 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1346 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1346 has 0 orthologous retrocopies within eutheria group .

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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,