RetrogeneDB ID: retro_ptro_1845

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:173757665..173758563(+)
• Located in intron of: ENSPTRG00000015610

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM20B
• Ensembl ID: ENSPTRG00000001725
• Aliases: None
• Description: None

Sequence

>retro_ptro_1845
ATACATCAACTGCCAAGCAGCGTTTCACTACTTGATCCCCTGAGGGCTTTTCACCGACTGATGACTGGCTTGTGGATGGA
GCTGTCACCCAAGTTGGACCACATGTTGCAGTCTTCCTAGGAGATTGCAGCCCAGTGGGTGGTTCCCCAGGAAGTGTACT
GTGAAGAGACACCAGAGCTGGGGGCAATCATGCATGCCATGGCCACCAAGCAAATTATTAAAGCTGATGTGGGTTATAAA
GGGACACAGCTAGCCTTACTGATCCTTGAAAGGGAACAGAAAGTTGTTTTCGAACCTAAGTAGTATAGCCGAGACTATGT
AGTGGAAGGGAACCATATGCCGGTTATGATAGACACAATGCGGAGGTAGCAGCCTTTCACTTGGACAGGATTGTGGGTGT
CCCAGAGCCCTGCTGATGGTGGGCAGATCCGTTCATCTTCACACAGAGATCAAGCCTGTTACCATGGAGCAGCTGTTGAG
CCCCTTCCTAACTGTAGGAAACAATACTTGTTTTTATGGGAAGTGTTATTACTACCGAGAAACAGAATCAGCTTGTGCCG
ATGGAGACACAATGGAAAAATCTGTCACACTTTGGCTTCCAGATGTGTGGCCTCTCCAGAAACACTGACACCCATGGGCC
AGGACTTACTGAAAAGGCAAATTGGCCAGGTGGGAGTATGATGAGCGCTACTGTGAGGCTGTGAAGAAAACGTCCCTTTA
TGACTCTGGCCTGTGCCGCCTGGACACCATTAACACAGCTGTCTTTGATTACCTCATTGACAATGCTGACTGCCATTACT
ATAAGAACTTTCAAGATAATGAGGGCGCCAGTATGCTCATCCTTCTTGATAACAACAAAAGCTTTGGGAACCCCTTGCTG
GATGAAAGAAGCATTCTT

Alignment

ORF - retro_ptro_1845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.88 %
• Parental protein coverage: 73.59 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IDNLDTSAANREDQRAFHRMMTGLRVELAPKLDHTLQSPWEIAAQWVVPREVYPEETPELGAIMHAMATK
          I..L..S.......RAFHR.MTGL..EL.PKLDH.LQS..EIAAQWVVP.EVY.EETPELGAIMHAMATK
Retrocopy IHQLPSSVSLLDPLRAFHRLMTGLWMELSPKLDHMLQSS*EIAAQWVVPQEVYCEETPELGAIMHAMATK

Parental  KIIKADVGYKGTQLKALLILEGGQKVVFKPKRYSRDHVVEG-EPYAGYDRHNAEVAAFHLDRILGFR-RA
          .IIKADVGYKGTQL.ALLILE..QKVVF.PK.YSRD.VVEG.EPYAGYDRHNAEVAAFHLDRI.G...RA
Retrocopy QIIKADVGYKGTQL-ALLILEREQKVVFEPK*YSRDYVVEG<EPYAGYDRHNAEVAAFHLDRIVGVP<RA

Parental  PLVVGRFVNLRTEIKPVATEQLLSTFLTVGNNTCFYGKCYYCRETEPACADGDIMEGSVTLWLPDVWPLQ
          .L.VGR.V.L.TEIKPV..EQLLS.FLTVGNNTCFYGKCYY.RETE.ACADGD.ME.SVTLWLPDVWPLQ
Retrocopy LLMVGRSVHLHTEIKPVTMEQLLSPFLTVGNNTCFYGKCYYYRETESACADGDTMEKSVTLWLPDVWPLQ

Parental  KHRHPWGRTYREGKLARWEYDESYCDAVKKTSPYDSGPRLLDIIDTAVFDYLIGNADRHHYESFQDDEGA
          KH.HPW.RTY..GKLARWEYDE.YC.AVKKTS.YDSG...LD.I.TAVFDYLI.NAD.H.Y..FQD.EGA
Retrocopy KH*HPWARTY*KGKLARWEYDERYCEAVKKTSLYDSGLCRLDTINTAVFDYLIDNADCHYYKNFQDNEGA

Parental  SMLILLDNAKSFGNPSLDERSIL
          SMLILLDN.KSFGNP.LDERSIL
Retrocopy SMLILLDNNKSFGNPLLDERSIL

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	0.02 RPM	73.23 RPM
SRP007412_cerebellum	0.00 RPM	71.16 RPM
SRP007412_heart	0.00 RPM	69.98 RPM
SRP007412_kidney	0.00 RPM	74.51 RPM
SRP007412_liver	0.00 RPM	32.14 RPM
SRP007412_testis	0.00 RPM	28.45 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1845 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1845 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1845 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2730
Pongo abelii	retro_pabe_2269

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005236	6 retrocopies	retro_chof_1509, retro_chof_1926, retro_chof_2615, retro_chof_2629, retro_chof_799, retro_chof_868,
Dasypus novemcinctus	ENSDNOG00000006175	2 retrocopies	retro_dnov_1484, retro_dnov_2346,
Echinops telfairi	ENSETEG00000005651	1 retrocopy	retro_etel_1128,
Homo sapiens	ENSG00000116199	1 retrocopy	retro_hsap_2730,
Gorilla gorilla	ENSGGOG00000002484	1 retrocopy	retro_ggor_1899,
Macropus eugenii	ENSMEUG00000006654	1 retrocopy	retro_meug_414,
Macaca mulatta	ENSMMUG00000006260	1 retrocopy	retro_mmul_1533,
Nomascus leucogenys	ENSNLEG00000015580	1 retrocopy	retro_nleu_592,
Otolemur garnettii	ENSOGAG00000012751	1 retrocopy	retro_ogar_2800,
Pongo abelii	ENSPPYG00000000466	2 retrocopies	retro_pabe_2268, retro_pabe_2269,
Pan troglodytes	ENSPTRG00000001725	1 retrocopy	retro_ptro_1845 ,
Ictidomys tridecemlineatus	ENSSTOG00000005086	2 retrocopies	retro_itri_441, retro_itri_539,
Tarsius syrichta	ENSTSYG00000005482	3 retrocopies	retro_tsyr_2065, retro_tsyr_2124, retro_tsyr_89,