RetrogeneDB ID: retro_ptro_2048

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:46518094..46518823(-)
• Located in intron of: ENSPTRG00000023645

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A14
• Ensembl ID: ENSPTRG00000022268
• Aliases: None
• Description: None

Sequence

>retro_ptro_2048
CAGCAAAGTACCACTGTAAGCCATGAGATGTCTCATCTGAACTGGAAACCCTTTGTATATGACACCTTGCCTCTATCACT
GCTGAGTTTGGAACTTTCCCCATGGACCTTGCCAAAACACGACTTCAGGTAGGTTCAAGGCCAAAGCATTGATGTCCGTT
TCAAAGAAACAAAATATAGACAGATGTTTCATGCTTTGTTTTGGATCTATAAAGAGGAAGGTGTATTGGCTCTGTATTCA
GGAATTGCTCCTGTTTTGCAAAGACAAGCATCATATGGCACCATTAAAATTGGGATTTACCAAAGCTTGAAGCAATTATT
TGTAGAACGTTTAGAAGATGAAACTCTTTTAATCAACATGACCTGTGGGGTAGTGTCAGGGGTGATATTTTCCACTATAG
CCAATCCCACCGATGTTCTAAAGATTCGAATGCAGGCTCAAGGAAGTTTGTTCCAAGGGAGCATGACTGGCAGCTTCATC
GATATATACCAACAGGAAGGCACCAGGGGTCTGTGGAGGAGTGTGGTTCCAACTGCTCAGCATGCTGCCATCGTTGTGGG
AGTAGAGCTACCAGTCTATGATTTTACTAAGAAGCACTTAATATTGTCAGGAATGATGGAAGACACAACTTTAACTCACT
TTGTTTCCAGCTTTACATGTGGTTTGGCTGGGGCTCTTGCCTCTAATCCAGGTGATGTGGCAGGCACTCACGTGATGAAC
CAGAGGGCT

Alignment

ORF - retro_ptro_2048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.31 %
• Parental protein coverage: 74.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QKSTTVSHEMSGLNWKPFVYGGL-ASIVAEFGTF-PVDLTKTRLQ-VQGQSIDARFKEIKYRGMFHALFR
          Q.STTVSHEMS.LNWKPFVY..L.ASI.AEFGTF.P..L.K.....VQGQSID.RFKE.KYR.MFHALF.
Retrocopy QQSTTVSHEMSHLNWKPFVYDTL<ASITAEFGTF>PWTLPKHDFR*VQGQSIDVRFKETKYRQMFHALFW

Parental  ICKEEGVLALYSGIAPALLRQASYGTIKIGIYQSLKRLFVERLEDETLLINMICGVVSGVISSTIANPTD
          I.KEEGVLALYSGIAP.L.RQASYGTIKIGIYQSLK.LFVERLEDETLLINM.CGVVSGVI.STIANPTD
Retrocopy IYKEEGVLALYSGIAPVLQRQASYGTIKIGIYQSLKQLFVERLEDETLLINMTCGVVSGVIFSTIANPTD

Parental  VLKIRMQAQGSLFQGSMIGSFIDIYQQEGTRGLWRGVVPTAQRAAIVVGVELPVYDITKKHLILSGMMGD
          VLKIRMQAQGSLFQGSM.GSFIDIYQQEGTRGLWR.VVPTAQ.AAIVVGVELPVYD.TKKHLILSGMM.D
Retrocopy VLKIRMQAQGSLFQGSMTGSFIDIYQQEGTRGLWRSVVPTAQHAAIVVGVELPVYDFTKKHLILSGMMED

Parental  TILTHFVSSFTCGLAGALASNPVDVVRTRMMNQRA
          T.LTHFVSSFTCGLAGALASNP.DV..T..MNQRA
Retrocopy TTLTHFVSSFTCGLAGALASNPGDVAGTHVMNQRA

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	0.13 RPM	16.53 RPM
SRP007412_cerebellum	0.18 RPM	11.36 RPM
SRP007412_heart	0.03 RPM	2.54 RPM
SRP007412_kidney	0.10 RPM	4.76 RPM
SRP007412_liver	0.07 RPM	2.75 RPM
SRP007412_testis	0.11 RPM	6.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2048 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2048 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2048 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2954
Pongo abelii	retro_pabe_2450

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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,