RetrogeneDB ID: retro_chof_1009

Retrocopy location

• Organism: Sloth (Choloepus hoffmanni)
• Coordinates: scaffold_183537:1004..1372(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RFK
• Ensembl ID: ENSCHOG00000009540
• Aliases: None
• Description: riboflavin kinase [Source:HGNC Symbol;Acc:30324]

Sequence

>retro_chof_1009
GTAGTGGATAATCTTCCAGCTGGTGTATCCGCTGGCATTCGTTATGGTTGGGTCCGTGTTGGAAGTGAAGCTGTCCGTGA
GATGGCGGTGAGCGCAGGGTGGAACCCACACTACAAGAATACAAAAAAGTCCGTGGGAACTCACATTTATGCATATCTTC
GAAGAGGACTTTTTTGGGGAATGCTCAATGTGGCCATCATTGGTACCTCAGACCAGAAAAGAACTTTGATTCTTTAGTGT
CATTTATTCCAGCAATTCAAGTTGATATTGAGGAAGTTAAGAAATGACTAGAATTGCCAGAACATTTGAAACTTAAAGAA
GAAAATTTCTTCCAGGTTCCTAAAAGCAAAATAATGAATGGCCACTGC

Alignment

ORF - retro_chof_1009 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.4 %
• Parental protein coverage: 96.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VVDNLPADISTGIYYGWASVGSGDVHKMVVSIGWNPYYKNTKKSMETHI-IHTFKEDFYGE-MLNVAIVG
          VVDNLPA..S.GI.YGW..VGS..V..M.VS.GWNP.YKNTKKS..THI..H.F.EDF.GE.MLNVAI.G
Retrocopy VVDNLPAGVSAGIRYGWVRVGSEAVREMAVSAGWNPHYKNTKKSVGTHI>MHIFEEDFFGE<MLNVAIIG

Parental  -YIRPEKNFDSLESLISAIQGDIEEAKKQLELPEHLKLKEDNFFQVPKSKIMNGHC
          .Y.RPEKNFDSL.S.I.AIQ.DIEE.KK.LELPEHLKLKE.NFFQVPKSKIMNGHC
Retrocopy <YLRPEKNFDSLVSFIPAIQVDIEEVKK*LELPEHLKLKEENFFQVPKSKIMNGHC

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Choloepus hoffmanni was not studied using RNA-Seq expression data.

ChIP-Seq

Choloepus hoffmanni was not studied using ChIP-Seq data.

EST

Choloepus hoffmanni was not studied using EST data.

TSS

Choloepus hoffmanni was not studied using FANTOM5 data.

Lab

retro_chof_1009 was not experimentally validated.

Homology

Retrocopy orthology:

Choloepus hoffmanni does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,