RetrogeneDB ID: retro_ptro_2143

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:39798063..39798938(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A4
• Ensembl ID: ENSPTRG00000016646
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4 [Source:HGNC Symbol;Acc:10990]

Sequence

>retro_ptro_2143
GACTTTCTGGCAGGTGGCGTGGCTGCGGCCATATCCAAGAACACAGCAGTGCCCATCAAGTGGGTCAAGCTGCTGCTGCA
AGTGCAGCATGCCAGCAAGCAGATCACCGCAGATAAGCTATGCAAGGACTAGACAGACTCTGTGGTTCATACCCCCAAGG
AGCAGGGAGTCCTGTCCTTCTGCCACGGTAACCTGGCCAGTGTCATCAGATACTTACCCACCTAGGCTGTCAACTTTGCC
CAAGGTAAACAGAAGCAGATCTTCTGAGGTGGGGTGGACGAGAGGCCCCAGTTGTGGTGCTACATTGCAGGCAATCTGGC
CCCCAGTGATGCCACTGGGCCACATCCTTGTGTATGGTGTACCCTCTTGATTTTCGCAGCTACTTGACTTTGTACCTGTC
TAGCAGCTAATGTGGGTAAAGCTAGAGCTGAAAGGGAATCCAGAAGCCTCAGTAACTGCCTGGTTAAGATCTACAAATCC
GATGGAATTAAGAGACTGAACCAAGGCTTTAACGTGTCAGTGTGGGGTATTATCATCTACCAAGCTCCCTACTTTGGTAT
CCATGACACTGCAAAAGGCATTTTTTCAGATCCCAAGAATGCTAACATCTTCATCAGCTGATGATCGCACAATCTGTCAC
TGGCATTGCTGGGATAAAAAGTCATTCCTATCCATTTGATACTGTTTGCCACCACAAGATGACATGGTCAGGGTTCAAAG
GAACTGATATTCTGCACACAGGCATCCCTGACTGCTGGAGGAAAATTGCTCATGATGAAGGAGACAAAGCTTTTCTCAAA
GGTGCATGGTCCAGCATTCTCAGAGGCATGGGTGGTGCTTCTATGCTTTTCTTATATGATAAAATAAAGAAGTAC

Alignment

ORF - retro_ptro_2143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.56 %
• Parental protein coverage: 96.63 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DFFAGGVAAAVSKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSFWRGNLANVIR
          DF.AGGVAAA.SK....PI..VKLLLQVQHASKQI.A.K..K...D.VV..PKEQG.LSF..GNLA.VIR
Retrocopy DFLAGGVAAAISKNTAVPIKWVKLLLQVQHASKQITADKLCKD*TDSVVHTPKEQGVLSFCHGNLASVIR

Parental  YFPTQALNFAFKDKYKQLFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFAR----TRLAADVG
          Y.PT.A.NFA...K.KQ.F.GGVD...Q.W.Y.AGNLA...A.G.........L.FA.....T.LAA.VG
Retrocopy YLPT*AVNFA-QGKQKQIF*GGVDERPQLWCYIAGNLAPSDATGPHPCVWCTLLIFAAT*LCTCLAANVG

Parental  KGAAQREFHGLGDCIIKIFKSDGLRGLYQGFNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHIFVS-WM
          K..A.RE...L..C..KI.KSDG...L.QGFNVSV.GIIIY.A.YFG..DTAKG...DPKN..IF.S..M
Retrocopy KARAERESRSLSNCLVKIYKSDGIKRLNQGFNVSVWGIIIYQAPYFGIHDTAKGIFSDPKNANIFIS<LM

Parental  IAQSVTAVAGLV--SYPFDTVRRRMMMQSGRKGADIMYTGTVDCWRKIAKDEGAKAFFKGAWSNVLRGMG
          IAQSVT..AG....SYPFDTV....M..SG.KG.DI..TG..DCWRKIA.DEG.KAF.KGAWS..LRGMG
Retrocopy IAQSVTGIAGIKSHSYPFDTVCHHKMTWSGFKGTDILHTGIPDCWRKIAHDEGDKAFLKGAWSSILRGMG

Parental  GAFVLVLYDEIKKY
          GA..L.LYD.IKKY
Retrocopy GASMLFLYDKIKKY

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	104.55 RPM
SRP007412_cerebellum	0.04 RPM	87.54 RPM
SRP007412_heart	0.00 RPM	955.76 RPM
SRP007412_kidney	0.05 RPM	81.91 RPM
SRP007412_liver	0.10 RPM	50.80 RPM
SRP007412_testis	0.00 RPM	8.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2143 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2143 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2143 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3336
Macaca mulatta	retro_mmul_2090

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013208	1 retrocopy	retro_btau_1592,
Choloepus hoffmanni	ENSCHOG00000010542	3 retrocopies	retro_chof_1117, retro_chof_1777, retro_chof_807,
Dasypus novemcinctus	ENSDNOG00000007258	3 retrocopies	retro_dnov_1531, retro_dnov_1800, retro_dnov_390,
Dipodomys ordii	ENSDORG00000013787	1 retrocopy	retro_dord_268,
Erinaceus europaeus	ENSEEUG00000001021	2 retrocopies	retro_eeur_274, retro_eeur_36,
Macropus eugenii	ENSMEUG00000008508	4 retrocopies	retro_meug_222, retro_meug_549, retro_meug_6, retro_meug_921,
Microcebus murinus	ENSMICG00000010865	1 retrocopy	retro_mmur_1356,
Oryctolagus cuniculus	ENSOCUG00000002594	1 retrocopy	retro_ocun_102,
Ochotona princeps	ENSOPRG00000005957	6 retrocopies	retro_opri_1154, retro_opri_146, retro_opri_377, retro_opri_517, retro_opri_543, retro_opri_685,
Pan troglodytes	ENSPTRG00000016646	9 retrocopies	retro_ptro_146, retro_ptro_1588, retro_ptro_2143 , retro_ptro_2364, retro_ptro_2388, retro_ptro_2517, retro_ptro_2525, retro_ptro_2819, retro_ptro_2882,
Pteropus vampyrus	ENSPVAG00000015279	1 retrocopy	retro_pvam_892,
Sarcophilus harrisii	ENSSHAG00000000932	1 retrocopy	retro_shar_160,
Tarsius syrichta	ENSTSYG00000004233	1 retrocopy	retro_tsyr_27,