RetrogeneDB ID: retro_ptro_1514

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 22:39496793..39497175(-)
• Located in intron of: ENSPTRG00000014412

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFK
• Ensembl ID: ENSPTRG00000021036
• Aliases: None
• Description: Riboflavin kinase [Source:UniProtKB/TrEMBL;Acc:K7BEG2]

Sequence

>retro_ptro_1514
AATTTTCCTGAGCAAGTGGTAGATAATCTGCCAGCCGATATATCCAGTGGCATTTATTATGGTTGGGCCAGTGCTGGAAG
TAGAGATGGTCAGAAGATGGTGGTGGGCATAGGATGGAACCCATACTATGAGAATACGAAGAAGTCCATGGAAACACATA
CCATGCATACCTTCAAAGAGCACTTCTATGGGGAAATCCTGAATGTGGCCATTGTTGGCTACCTCAGACCAGAAAAGAAC
TTTGATTCATGAGAGTCACTTATTTCAGCAATTCAAGGTGATTTTTGAGGAAGCTAAGAAATGACTAGATTTACCAGAAC
ATTTGAAACTCAAAGAAGACAATTTCTTCCAGGTTTCTAAAAGCAAAATAATGAATGGCCAC

Alignment

ORF - retro_ptro_1514 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.28 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NFPEQVVDNLPADISTGIYYGWASVGSGDVHKMVVSIGWNPYYKNTKKSMETHIMHTFKEDFYGEILNVA
          NFPEQVVDNLPADIS.GIYYGWAS.GS.D..KMVV.IGWNPYY.NTKKSMETH.MHTFKE.FYGEILNVA
Retrocopy NFPEQVVDNLPADISSGIYYGWASAGSRDGQKMVVGIGWNPYYENTKKSMETHTMHTFKEHFYGEILNVA

Parental  IVGYLRPEKNFDSLESLISAIQGD-IEEAKKRLELPEHLKIKEDNFFQVSKSKIMNGH
          IVGYLRPEKNFDS.ESLISAIQGD..EEAKK.L.LPEHLK.KEDNFFQVSKSKIMNGH
Retrocopy IVGYLRPEKNFDS*ESLISAIQGD>FEEAKK*LDLPEHLKLKEDNFFQVSKSKIMNGH

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	25.52 RPM
SRP007412_cerebellum	0.18 RPM	16.88 RPM
SRP007412_heart	0.03 RPM	11.92 RPM
SRP007412_kidney	0.05 RPM	13.73 RPM
SRP007412_liver	0.07 RPM	10.31 RPM
SRP007412_testis	0.42 RPM	58.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1514 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1514 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1514 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2590
Callithrix jacchus	retro_cjac_654

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 77 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003553	1 retrocopy	retro_amel_611,
Choloepus hoffmanni	ENSCHOG00000009540	35 retrocopies	retro_chof_1009, retro_chof_1035, retro_chof_1036, retro_chof_1399, retro_chof_1415, retro_chof_1426, retro_chof_1506, retro_chof_1743, retro_chof_1816, retro_chof_182, retro_chof_1898, retro_chof_2088, retro_chof_210, retro_chof_2122, retro_chof_2138, retro_chof_2139, retro_chof_218, retro_chof_2283, retro_chof_2307, retro_chof_2600, retro_chof_2651, retro_chof_2675, retro_chof_302, retro_chof_372, retro_chof_374, retro_chof_404, retro_chof_497, retro_chof_523, retro_chof_633, retro_chof_640, retro_chof_75, retro_chof_834, retro_chof_882, retro_chof_927, retro_chof_983,
Callithrix jacchus	ENSCJAG00000031816	3 retrocopies	retro_cjac_2553, retro_cjac_4032, retro_cjac_654,
Homo sapiens	ENSG00000135002	5 retrocopies	retro_hsap_2590, retro_hsap_2693, retro_hsap_2828, retro_hsap_305, retro_hsap_532,
Gorilla gorilla	ENSGGOG00000010358	1 retrocopy	retro_ggor_339,
Macropus eugenii	ENSMEUG00000000988	6 retrocopies	retro_meug_1179, retro_meug_1815, retro_meug_1922, retro_meug_2144, retro_meug_268, retro_meug_698,
Monodelphis domestica	ENSMODG00000001904	2 retrocopies	retro_mdom_1404, retro_mdom_194,
Nomascus leucogenys	ENSNLEG00000002051	4 retrocopies	retro_nleu_1502, retro_nleu_1523, retro_nleu_1787, retro_nleu_2401,
Pongo abelii	ENSPPYG00000019302	5 retrocopies	retro_pabe_1224, retro_pabe_1622, retro_pabe_1763, retro_pabe_217, retro_pabe_2289,
Pan troglodytes	ENSPTRG00000021036	3 retrocopies	retro_ptro_1514 , retro_ptro_246, retro_ptro_398,
Pteropus vampyrus	ENSPVAG00000014032	4 retrocopies	retro_pvam_1063, retro_pvam_255, retro_pvam_347, retro_pvam_951,
Sarcophilus harrisii	ENSSHAG00000015887	3 retrocopies	retro_shar_79, retro_shar_85, retro_shar_99,
Tursiops truncatus	ENSTTRG00000014859	4 retrocopies	retro_ttru_1624, retro_ttru_164, retro_ttru_1822, retro_ttru_95,
Vicugna pacos	ENSVPAG00000002619	1 retrocopy	retro_vpac_360,