RetrogeneDB ID: retro_ptro_2388

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:122828101..122828840(+)
• 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_2388
TTCAAGGGCTTCCTGGCAGGTAGAGTGGCCACGGCCATCTCCAAGACGGAGGTTGCTCCCATCAAGCGGATCAAGCTGCT
GCTGCAGGTGCAGCGTGCCAGCAAGCAGATCACCGCAGATAAGCAATACAAGGGCATTATAGACCATATAGGTCGGTATT
CTCAAGGAGCAGGGAGTCCTGTCCTTCTGGCGCAGTAACCTGGCCAATGTCATCAGATACTTCCCCACCCAGGCTCTTAA
CTTTGCTTTCAAAGATAAATAAAAGCAGATCTTCCTGGGTGGTGTGGACAAGAGGATCCAGTTTTGGCGCTACTTTGAAG
GGAATCTGGCATCAAGCAGTGTTTCTGGGGCCACATCCTTTTGTTATGTGTACCCTCTTGATTTTGCCCATCTAGCAGCC
GATGTGGGTAAAGCTGGAGCTGAAAGGGAATTCTGAGGCCTCGGTGACTGCCTGGTTAAGATCTACAAATCTGATGGGAT
TAAGGGCCTGTACCAAGGCTTTCACGTGTCTGTGCAGGGTATTATCATCTACCGAGCTGCCTACTTCAGTATCTATGACA
CTGCAAAGGGAATGCTTCCAGATCCCAAGAACACTTACATCATCATCAGCCAGATGATCGCAAAGACTATCACTGCCATT
GCTGGGTTGACTTCCTATCCATTTGACACCATTGGCTGCCACATGATGATGCAGTCAGGGTGCAAAGGAACTGACATCAT
GTACACAGGCATGCTTGAC

Alignment

ORF - retro_ptro_2388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.3 %
• Parental protein coverage: 83.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLDFFAGGVAAAVSKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVR-IPKEQGFLSFWRGNLAN
          F..F.AG.VA.A.SKT.VAPI.R.KLLLQVQ.ASKQI.A.KQYKGIID...R.I.KEQG.LSFWR.NLAN
Retrocopy FKGFLAGRVATAISKTEVAPIKRIKLLLQVQRASKQITADKQYKGIIDHIGR>ILKEQGVLSFWRSNLAN

Parental  VIRYFPTQALNFAFKDKYKQLFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFARTRLAADVGK
          VIRYFPTQALNFAFKDK.KQ.FLGGVD...QFWRYF.GNLAS....GATS.C.VYPLDFA...LAADVGK
Retrocopy VIRYFPTQALNFAFKDK*KQIFLGGVDKRIQFWRYFEGNLASSSVSGATSFCYVYPLDFAH--LAADVGK

Parental  GAAQREFHGLGDCIIKIFKSDGLRGLYQGFNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHIFVSWMIA
          ..A.REF.GLGDC..KI.KSDG..GLYQGF.VSVQGIIIYRAAYF..YDTAKGMLPDPKN..I..S.MIA
Retrocopy AGAEREF*GLGDCLVKIYKSDGIKGLYQGFHVSVQGIIIYRAAYFSIYDTAKGMLPDPKNTYIIISQMIA

Parental  QSVTAVAGLVSYPFDTVRRRMMMQSGRKGADIMYTGTVD
          ...TA.AGL.SYPFDT....MMMQSG.KG.DIMYTG..D
Retrocopy KTITAIAGLTSYPFDTIGCHMMMQSGCKGTDIMYTGMLD

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	1.14 RPM	104.55 RPM
SRP007412_cerebellum	1.29 RPM	87.54 RPM
SRP007412_heart	0.76 RPM	955.76 RPM
SRP007412_kidney	5.73 RPM	81.91 RPM
SRP007412_liver	2.23 RPM	50.80 RPM
SRP007412_testis	0.32 RPM	8.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2388 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2388 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2388 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3516
Gorilla gorilla	retro_ggor_2377

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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,