RetrogeneDB ID: retro_pabe_3595

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:43993776..43994350(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A14
• Ensembl ID: ENSPPYG00000020715
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier, brain), member 14 [Source:HGNC Symbol;Acc:10984]

Sequence

>retro_pabe_3595
TTTGTATAACGTTTAGAAGATGAAACTCTTTTAATTAACATGACCTGTGGGGTAGTGTCAGGAGTGATATTTTCCACTAT
AGCCAATCCCACCGATGTTCTAAAGATTTGAATGCAGGCTCAAGGAAGTTTGTTCCAAGGGAGCATGACTGGCAGCTTCA
TCGATATATACCAACAGGAAGGCACCAGGTGTCTGTGGAGGGGTGTGGTTCCAACTGCTCAGCATGCTGCCATCGTTGTG
GGAGTAGAGCTACCAGTCTATGATTTTACTAAGAAGCACTTAATATTGTCAGGAATGATGGAAGACACAACTTTAACTCA
CTTTGTTTCCAGCTTTACGTGTGGTTTGGCTGGGGCTCTTGCCTCTAATCCAGGTGATGTGGCAGGCACTCGCATGATGA
ACCAGAGGGCAATCGTGGGATATGTGGATCTCTATAAGGACACTTTGGATGGTATTTTAAAGATGTGGAAACACGAGGGC
TTTTTTGTACTCTAAAGGATTTTGGCCAAACTGGCTTTGGCTTGGACCCTGGAACATCATTCTTTAAATTACATATGAGT
AGCTCAAGAGGCTT

Alignment

ORF - retro_pabe_3595 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.02 %
• Parental protein coverage: 59.08 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FVERLEDETLLINMICGVVSGVISSTIANPTDVLKIRMQAQGSLFQGSMIGSFIDIYQQEGTRGLWRGVV
          FV.RLEDETLLINM.CGVVSGVI.STIANPTDVLKI.MQAQGSLFQGSM.GSFIDIYQQEGTR.LWRGVV
Retrocopy FV*RLEDETLLINMTCGVVSGVIFSTIANPTDVLKI*MQAQGSLFQGSMTGSFIDIYQQEGTRCLWRGVV

Parental  PTAQRAAIVVGVELPVYDITKKHLILSGMMGDTILTHFVSSFTCGLAGALASNPVDVVRTRMMNQRAIVG
          PTAQ.AAIVVGVELPVYD.TKKHLILSGMM.DT.LTHFVSSFTCGLAGALASNP.DV..TRMMNQRAIVG
Retrocopy PTAQHAAIVVGVELPVYDFTKKHLILSGMMEDTTLTHFVSSFTCGLAGALASNPGDVAGTRMMNQRAIVG

Parental  HVDLYKGTVDGILKMWKHEGFFAL-YKGFWPNWLRLGP-WNIIFFITYEQLKRL
          .VDLYK.T.DGILKMWKHEGFF.L..K.F......L.P.WNII..ITYE.LKRL
Retrocopy YVDLYKDTLDGILKMWKHEGFFVL<LKDFGQTGFGLDP<WNIIL*ITYE*LKRL

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	0.06 RPM	19.57 RPM
SRP007412_cerebellum	0.00 RPM	19.70 RPM
SRP007412_heart	0.00 RPM	1.96 RPM
SRP007412_kidney	0.00 RPM	6.63 RPM
SRP007412_liver	0.00 RPM	2.66 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3595 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3595 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3595 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016263	1 retrocopy	retro_btau_1362,
Canis familiaris	ENSCAFG00000018766	1 retrocopy	retro_cfam_1359,
Callithrix jacchus	ENSCJAG00000002456	1 retrocopy	retro_cjac_2257,
Homo sapiens	ENSG00000102078	1 retrocopy	retro_hsap_2954,
Macaca mulatta	ENSMMUG00000008386	1 retrocopy	retro_mmul_1943,
Nomascus leucogenys	ENSNLEG00000015318	1 retrocopy	retro_nleu_1638,
Pongo abelii	ENSPPYG00000020715	2 retrocopies	retro_pabe_2450, retro_pabe_3595 ,
Pan troglodytes	ENSPTRG00000022268	1 retrocopy	retro_ptro_2048,
Tursiops truncatus	ENSTTRG00000016206	2 retrocopies	retro_ttru_1159, retro_ttru_1570,