RetrogeneDB ID: retro_pabe_1224

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:30306751..30307216(+)
• Located in intron of: ENSPPYG00000006311

Retrocopy information

• Ensembl ID: ENSPPYG00000006312
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RFK
• Ensembl ID: ENSPPYG00000019302
• Aliases: None
• Description: riboflavin kinase [Source:HGNC Symbol;Acc:30324]

Sequence

>retro_pabe_1224
CTGTCCCCCGCGTCGACGGCGGCTCCACAGGACGCGCAGACCGGGCCGCAGCCCATGCCCCGAGCGGACTGCATTATGAC
GCACCTGCCTTACTTCTGCCGGGGCCAAGTCGTGCGGGGCTTCGGCCGCGGCTCCAAGCAGCTGGGCATCCCCACAGCTA
ATTTTCCTGAGCAAGTGGTAGATAATCTTCCAGCTGATATATCCACCGGTATTTACTATGGTTGGGCCAGTGTTGGAAGT
GGAGATGTCCATAAGATGGTGGTGAGCATAGGATGGAACCCATATTACAAGAATACGAAGAAGTCTATGGAAACACATAT
CATGCATACCTTCAAAGAGGACTTCTATGGGGAAATCCTCAATGTGGCCATTGTTGGCTACCTGAGACCAGAAAAGAACT
TTGATTCTTTAGAGTCACTTATTTCAGCAATTCAAGGTGATATTGAAGAAGCTAAGAAACGACTA

Alignment

ORF - retro_pabe_1224 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.06 %
• Parental protein coverage: 54.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGTASTAAPQDAQTGPQPMPRADCIMRHLPYFCRGQVVRGFGRGSKQLGIPTANFPEQVVDNLPADISTG
          L..ASTAAPQDAQTGPQPMPRADCIM.HLPYFCRGQVVRGFGRGSKQLGIPTANFPEQVVDNLPADISTG
Retrocopy LSPASTAAPQDAQTGPQPMPRADCIMTHLPYFCRGQVVRGFGRGSKQLGIPTANFPEQVVDNLPADISTG

Parental  IYYGWASVGSGDVHKMVVSIGWNPYYKNTKKSMETHIMHTFKEDFYGEILNVAIVGYLRPEKNFDSLESL
          IYYGWASVGSGDVHKMVVSIGWNPYYKNTKKSMETHIMHTFKEDFYGEILNVAIVGYLRPEKNFDSLESL
Retrocopy IYYGWASVGSGDVHKMVVSIGWNPYYKNTKKSMETHIMHTFKEDFYGEILNVAIVGYLRPEKNFDSLESL

Parental  ISAIQGDIEEAKKRL
          ISAIQGDIEEAKKRL
Retrocopy ISAIQGDIEEAKKRL

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	0.11 RPM	14.71 RPM
SRP007412_cerebellum	0.12 RPM	12.77 RPM
SRP007412_heart	0.03 RPM	6.35 RPM
SRP007412_kidney	0.00 RPM	14.42 RPM
SRP007412_liver	0.09 RPM	11.08 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1224 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1224 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 90 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,
Erinaceus europaeus	ENSEEUG00000015769	1 retrocopy	retro_eeur_425,
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,
Mus musculus	ENSMUSG00000024712	1 retrocopy	retro_mmus_3439,
Nomascus leucogenys	ENSNLEG00000002051	4 retrocopies	retro_nleu_1502, retro_nleu_1523, retro_nleu_1787, retro_nleu_2401,
Oryctolagus cuniculus	ENSOCUG00000001622	1 retrocopy	retro_ocun_591,
Otolemur garnettii	ENSOGAG00000013120	5 retrocopies	retro_ogar_1435, retro_ogar_1475, retro_ogar_3257, retro_ogar_725, retro_ogar_735,
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,
Rattus norvegicus	ENSRNOG00000022273	5 retrocopies	retro_rnor_1099, retro_rnor_1899, retro_rnor_2212, retro_rnor_2828, retro_rnor_2863,
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,