RetrogeneDB ID: retro_pabe_2450

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:87091466..87092358(+)
• Located in intron of: ENSPPYG00000014898

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_2450
CAGAGAAGTACCACTGTAAGCCATGAGATGTCTCGTCTGAACTGGAAACCCTTTGTATATGACGCCTTGCCTCTATCATT
GCTGAGTTTGGAACTTTCCCCAGGGACCTTGCCAAAACACTACTTCAGGTAGGTTCAAGGCCAAAGCATTGATGTCCGTT
TCAAAGAAACAAAATATAGATGGATGTTTCATGCTTTGTTTTGGATCTATAAAGAGGAAGGTGTATTGGCTCTGTATTCA
GGAATTGCTCCTGTTTTGTGAAGACAAGCATCATATGGCACCATTAAAATTGGGATTTACCAAAGCTTGAAGCAATTATT
TGTATAACGTTTAGAAGATGAAACTCTTTTAATTAACATGACCTGTGGGGTAGTGTCAGGAGTGATATTTTCCACTATAG
CCAATCCCACCGATGTTCTAAAGATTTGAATGCAGGCTCAAGGAAGTTTGTTCCAAGGGAGCATGACTGGCAGCTTCATC
GATATATACCAACAGGAAGGCACCAGGTGTCTGTGGAGGGGTGTGGTTCCAACTGCTCAGCATGCTGCCATCGTTGTGGG
AGTAGAGCTACCAGTCTATGATTTTACTAAGAAGCACTTAATATTGTCAGGAATGATGGAAGACACAACTTTAACTCACT
TTGTTTCCAGCTTTACGTGTGGTTTGGCTGGGGCTCTTGCCTCTAATCCAGGTGATGTGGCAGGCACTCGCATGATGAAC
CAGAGGGCAATCGTGGGATATGTGGATCTCTATAAGGACACTTTGGATGGTATTTTAAAGATGTGGAAACACGAGGGCTT
TTTTGTACTCTAAAGGATTTTGGCCAAACTGGCTTTGGCTTGGACCCTGGAACATCATTCTTTAAATTACGTATGAGTAG
CTCAAGAGGCTT

Alignment

ORF - retro_pabe_2450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.12 %
• Parental protein coverage: 91.38 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QKSTTVSHEMSGLNWKPFVYGGL-ASIVAEFGTF-PVDLTKTRLQ-VQGQSIDARFKEIKYRGMFHALFR
          Q.STTVSHEMS.LNWKPFVY..L.ASI.AEFGTF.P..L.K.....VQGQSID.RFKE.KYR.MFHALF.
Retrocopy QRSTTVSHEMSRLNWKPFVYDAL<ASIIAEFGTF>PGTLPKHYFR*VQGQSIDVRFKETKYRWMFHALFW

Parental  ICKEEGVLALYSGIAPALLRQASYGTIKIGIYQSLKRLFVERLEDETLLINMICGVVSGVISSTIANPTD
          I.KEEGVLALYSGIAP.L.RQASYGTIKIGIYQSLK.LFV.RLEDETLLINM.CGVVSGVI.STIANPTD
Retrocopy IYKEEGVLALYSGIAPVL*RQASYGTIKIGIYQSLKQLFV*RLEDETLLINMTCGVVSGVIFSTIANPTD

Parental  VLKIRMQAQGSLFQGSMIGSFIDIYQQEGTRGLWRGVVPTAQRAAIVVGVELPVYDITKKHLILSGMMGD
          VLKI.MQAQGSLFQGSM.GSFIDIYQQEGTR.LWRGVVPTAQ.AAIVVGVELPVYD.TKKHLILSGMM.D
Retrocopy VLKI*MQAQGSLFQGSMTGSFIDIYQQEGTRCLWRGVVPTAQHAAIVVGVELPVYDFTKKHLILSGMMED

Parental  TILTHFVSSFTCGLAGALASNPVDVVRTRMMNQRAIVGHVDLYKGTVDGILKMWKHEGFFAL-YKGFWPN
          T.LTHFVSSFTCGLAGALASNP.DV..TRMMNQRAIVG.VDLYK.T.DGILKMWKHEGFF.L..K.F...
Retrocopy TTLTHFVSSFTCGLAGALASNPGDVAGTRMMNQRAIVGYVDLYKDTLDGILKMWKHEGFFVL<LKDFGQT

Parental  WLRLGP-WNIIFFITYEQLKRL
          ...L.P.WNII..ITYE.LKRL
Retrocopy GFGLDP<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	0.28 RPM	19.57 RPM
SRP007412_cerebellum	1.34 RPM	19.70 RPM
SRP007412_heart	0.03 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_2450 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2450 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2450 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2954
Pan troglodytes	retro_ptro_2048

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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,