RetrogeneDB ID: retro_ptro_2525

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:53093087..53093936(+)
• 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_2525
GACTTCCTGGCAGGTGGAGTGGCCGAAGCCATCTCCAAGACAGCGGTAGCGCCCATCGAGCAGGTCAAGCTGCTGCTGCA
GGTGCAGCATGCCAGCAAGCAGATCACCTCAGCTAAGCAATACAAGGGCATTATAGACTGCGTGGTCGTATTCCCAAGAA
GCAGGGAGTCCTGTCCTGGCGCGGTAACCTGGCCAATGCCATCAGATACTTCCCCACCCAGGCTTTTAACTTCGCCTTCA
AAGATAAATACAAGCAGATCTTCCTGGGTGGTGTGGACAAAAGACTCAGTTTGGGCGCTACTTTGCAGGGAATCTGGCAT
CAGGAGGTGCCGCTGGGGCCACATACTTGTGTTTTGTGTACCCTCTTGATTTTGCCCGTACCTGTCTAGCAGCTAATGTG
GGTAAAGCTGAAGCTGAAAGGGAATTCCGAGGCCTCTGTGACTGCCTGGTTAAGATCTACAAATCTGATGGGATTAAGGG
CCTGTACCAAGGCTTTAACGTGTCTGTGCAGAGTATTATCCGAGCTGCCTACTTCGGTATCTATGACACCGCAAAGGGAA
TGCTTCCGGATCCCAAGGACACTCACATCGTCATCAGCTGGATGACCACACAGACTGTCACTGCCTTTTCTAGGTTGACT
TCCTATTCATTTGACGTCGTTCGCCTCTCGTGATGATTCAGTCAGGGCGCAAAGTAACTGACATCATGTACACAGGCACA
CTTGACTGCTAGAGGAAGATTGCTGGTGATGAAGGAGGCAAAGCTTTTTTCAAGGGTTCATGGTCCAGTGTTCTCAGAGG
CATGGGTGGTGCTTTTGTGCTTGTCTTGTTTGATGAAATCAAGAAGTAC

Alignment

ORF - retro_ptro_2525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.28 %
• Parental protein coverage: 96.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DFFAGGVAAAVSKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVV-RIPKEQGFLSFWRGNLANVI
          DF.AGGVA.A.SKTAVAPIE.VKLLLQVQHASKQI...KQYKGIIDCVV.RIPK.QG.LS.WRGNLAN.I
Retrocopy DFLAGGVAEAISKTAVAPIEQVKLLLQVQHASKQITSAKQYKGIIDCVV<RIPKKQGVLS-WRGNLANAI

Parental  RYFPTQALNFAFKDKYKQLFLGGVDRH-KQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGKG
          RYFPTQA.NFAFKDKYKQ.FLGGVD....QF.RYFAGNLASGGAAGAT.LCFVYPLDFART.LAA.VGK.
Retrocopy RYFPTQAFNFAFKDKYKQIFLGGVDKR<TQFGRYFAGNLASGGAAGATYLCFVYPLDFARTCLAANVGKA

Parental  AAQREFHGLGDCIIKIFKSDGLRGLYQGFNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHIFVSWMIAQ
          .A.REF.GL.DC..KI.KSDG..GLYQGFNVSVQ.II..RAAYFG.YDTAKGMLPDPK..HI..SWM..Q
Retrocopy EAEREFRGLCDCLVKIYKSDGIKGLYQGFNVSVQSII--RAAYFGIYDTAKGMLPDPKDTHIVISWMTTQ

Parental  SVTAVAGLVSYPFDTVRRR-MMMQSGRKGADIMYTGTVDCWRKIAKDEGAKAFFKGAWSNVLRGMGGAFV
          .VTA...L.SY.FD.VR....M.QSGRK..DIMYTGT.DC.RKIA.DEG.KAFFKG.WS.VLRGMGGAFV
Retrocopy TVTAFSRLTSYSFDVVRLS<VMIQSGRKVTDIMYTGTLDC*RKIAGDEGGKAFFKGSWSSVLRGMGGAFV

Parental  LVLYDEIKKY
          LVL.DEIKKY
Retrocopy LVLFDEIKKY

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	7.47 RPM	104.55 RPM
SRP007412_cerebellum	2.62 RPM	87.54 RPM
SRP007412_heart	0.93 RPM	955.76 RPM
SRP007412_kidney	17.91 RPM	81.91 RPM
SRP007412_liver	5.01 RPM	50.80 RPM
SRP007412_testis	1.48 RPM	8.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2525 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2525 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2525 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3730
Gorilla gorilla	retro_ggor_2517
Pongo abelii	retro_pabe_3130

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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,