RetrogeneDB ID: retro_ptro_2882

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:32713699..32714561(-)
• 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_2882
GACTTCCTGGCAGGTGGTGTCACTGTGGCCATCCCCAAGATGGCAGTAGTGCCCATCGAGGGGGTCAAGTTGCTGCTGCA
GGTGCAGCATGCCAGCAAGCAAATCACCACAGATAAGCAATACAAAGGCATTATAGACTGTGTGGTCCGTATTCCCAAGG
AGCAGGGAGTCCTGTCCTTCTGGTGCAGTAACCTGGCCAATGTCATCAGATAATTCCCCACCCAGGCTCTCAACCTCACC
TTCAAAGATAAAAACAAGCAGATCTTCCTGGGTGGTGTGGACAAGAAGACCCAGTTTTGGCATGACTTTGCAGGGAATCT
GGCATCAGGCAGTGCCGCTGGGGCCACATCCTTATGTGTTGTGTACCCTCTTGGTTTTGCCCATACCTTTCTAGCAGCCG
ATGTGGGTAGACCTGGAGGCAAAAGGGGATTCAGAGATCTCGATGACTGCCTGGTTAAGATCTACAAATTGGATGGGATT
AAGGGCCTGTACCAAGGCTTTAACGTGCCTGTGCAGGGTATTGTCATCTACCAAGCTGTCTACTTCAGTATCTATGGCAC
TGTAAAGGGAATGCTTCCAGATCCCAAGAACACTCGCATCATCATCAGCTGGATGATGGCACAGTCCATCACTTCCGTTT
GCTGGGTTGACTTCCTATCCATTTGACACTGTTTGCCGCTGCATGATGATGCAGTCAGAACTCAAAGCAGCTGACATCAT
GTACACAGGCACACTTGACTGCTGGAGGGAGATTGCTCGTGATGAAGGAGACAAAGCTTTTTTCAAGGGTGCATGGTCCA
ATGTCCTCAGAGGCATGAGTGGTGCTTTTGTGCTTGTCTTGTGTGATGAAATCAAAAAGTAC

Alignment

ORF - retro_ptro_2882 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 96.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DFFAGGVAAAVSKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSFWRGNLANVIR
          DF.AGGV..A..K.AV.PIE.VKLLLQVQHASKQI...KQYKGIIDCVVRIPKEQG.LSFW..NLANVIR
Retrocopy DFLAGGVTVAIPKMAVVPIEGVKLLLQVQHASKQITTDKQYKGIIDCVVRIPKEQGVLSFWCSNLANVIR

Parental  YFPTQALNFAFKDKYKQLFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGKGAA
          .FPTQALN..FKDK.KQ.FLGGVD...QFW..FAGNLASG.AAGATSLC.VYPL.FA.T.LAADVG....
Retrocopy *FPTQALNLTFKDKNKQIFLGGVDKKTQFWHDFAGNLASGSAAGATSLCVVYPLGFAHTFLAADVGRPGG

Parental  QREFHGLGDCIIKIFKSDGLRGLYQGFNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHIFVSWMIAQSV
          .R.F..L.DC..KI.K.DG..GLYQGFNV.VQGI.IY.A.YF..Y.T.KGMLPDPKN..I..SWM.AQS.
Retrocopy KRGFRDLDDCLVKIYKLDGIKGLYQGFNVPVQGIVIYQAVYFSIYGTVKGMLPDPKNTRIIISWMMAQSI

Parental  TAV-AGLVSYPFDTVRRRMMMQSGRKGADIMYTGTVDCWRKIAKDEGAKAFFKGAWSNVLRGMGGAFVLV
          T.V.AGL.SYPFDTV.R.MMMQS..K.ADIMYTGT.DCWR.IA.DEG.KAFFKGAWSNVLRGM.GAFVLV
Retrocopy TSV>AGLTSYPFDTVCRCMMMQSELKAADIMYTGTLDCWREIARDEGDKAFFKGAWSNVLRGMSGAFVLV

Parental  LYDEIKKY
          L.DEIKKY
Retrocopy LCDEIKKY

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	1.52 RPM	104.55 RPM
SRP007412_cerebellum	1.33 RPM	87.54 RPM
SRP007412_heart	0.61 RPM	955.76 RPM
SRP007412_kidney	6.54 RPM	81.91 RPM
SRP007412_liver	2.46 RPM	50.80 RPM
SRP007412_testis	0.11 RPM	8.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2882 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2882 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2882 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4239
Gorilla gorilla	retro_ggor_2840
Pongo abelii	retro_pabe_3398

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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,