RetrogeneDB ID: retro_pabe_2848

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:29727715..29728814(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PANK3
• Ensembl ID: ENSPPYG00000016024
• Aliases: None
• Description: pantothenate kinase 3 [Source:HGNC Symbol;Acc:19365]

Sequence

>retro_pabe_2848
ATGAAGATCAAAGATGCCAAGAAACCCTCTTTCCCATGGTTTGGCATGTACATTGGGGGAACTCTAGTAAAGCTCTAGTA
CTTTGAACCTATTGATATCACAGCAGAGGAAGAACAAGAAGTTGAGAGTTTAAAAAGTATTCGAAAATATTTGACTTCTA
ATGTAGCATATGGATCCACCGGCATTTGGGATGTACACCTTGAACTGAAAAATTTAACACTTTTTGGCCAAAGAGAGAAC
TTGCACTTTACCAACTTTCCAACCCAGGACCTGCCTACTTTTATCCAAATGGGAAGAGATAAAAACTTCTCAACATTGCA
AACCGTGCTATGTGCTACAGGAGGTGGTGCCTACAAGTTTGAAAAAGATTTTCGCACAAACCTCCACCTGCACAAACTGG
ATGAACTTGACTGCCTTGTAAAGGGCTTGCTGTGTATAGACTCTGTCAGTTTCAATGGACAAGCGGAGTGCTGTTATTTA
GCTAATGCACAGAACCTCAGCGATGCCAAAAGATGCCTTTTAACCTGGATGATCCCTGGCCACTGCTTGTAGTGAACATT
GGCTCAGGAGTCAGTATTTCAGCAGTGCATTCCGAAGACAACTACAAACGAGTGACTGGGACAAGCCTTGGAGAGGGTAC
CTTTCTGGGTTTATGCAGTTTATTGACTGGCTGTGAAAGTTTTGAAGAGGCTCTTGAAATGGCATCCAAAGGTGACAGCA
CACAAGCTGACAAGCTGGCCCGTGATATTTATGGAGGAGGTCATGAAAGATTTGGTTTGCCAGGTTGGGCTGTAGCATCT
AGTTTTAGGAATATGATTTATAAGGAGAAGAGAGAATCTGTTAGTAAAGAAGATCTGGCAGAGCTACTTTAGTTACTATC
ACCAATAACTTTGGTTCTGTGGCACGAATGTGTGCTGTTAATGAGGAAATAAACAGAGTTGTCTTTGTTGGAAACGTTTT
ACGTGTCAACACCCTCTCAATGAAACTTTTGGCATATACACTGGATTTTTGGTCAAAAGGTCAACTGAAAGCATTGTTTC
TTGAACATGAGGGATACTTTGGAGCAGTTAGTGCACTTCTTGGGCTGCCAAATTTCAGC

Alignment

ORF - retro_pabe_2848 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKIKDAKKPSFPWFGMDIGGTLVKLSYFEPIDITAEEEQEEVESLKSIRKYLTSNVAYGSTGIRDVHLEL
          MKIKDAKKPSFPWFGM.IGGTLVKL.YFEPIDITAEEEQE.VESLKSIRKYLTSNVAYGSTGI.DVHLEL
Retrocopy MKIKDAKKPSFPWFGMYIGGTLVKL*YFEPIDITAEEEQE-VESLKSIRKYLTSNVAYGSTGIWDVHLEL

Parental  KDLTLFGRRGNLHFIRFPTQDLPTFIQMGRDKNFSTLQTVLCATGGGAYKFEKDFRTIGNLHLHKLDELD
          K.LTLFG.R.NLHF..FPTQDLPTFIQMGRDKNFSTLQTVLCATGGGAYKFEKDFRT..NLHLHKLDELD
Retrocopy KNLTLFGQRENLHFTNFPTQDLPTFIQMGRDKNFSTLQTVLCATGGGAYKFEKDFRT--NLHLHKLDELD

Parental  CLVKGLLYIDSVSFNGQAECYYFANA-SEPERCQKMPFNLDDPYPLLVVNIGSGVSILAVHSKDNYKRVT
          CLVKGLL.IDSVSFNGQAEC.Y.ANA..EP.RCQKMPFNLDDP.PLLVVNIGSGVSI.AVHS.DNYKRVT
Retrocopy CLVKGLLCIDSVSFNGQAECCYLANA<TEPQRCQKMPFNLDDPWPLLVVNIGSGVSISAVHSEDNYKRVT

Parental  GTSLGGGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMIYKE
          GTSLG.GTFLGLCSLLTGCESFEEALEMASKGDSTQADKL.RDIYGG..ERFGLPGWAVASSF.NMIYKE
Retrocopy GTSLGEGTFLGLCSLLTGCESFEEALEMASKGDSTQADKLARDIYGGGHERFGLPGWAVASSFRNMIYKE

Parental  KRESVSKEDLA-RATLVTITNNIGSVARMCAVNEKINRVVFVGNFLRVNTLSMKLLAYALDYWSKGQLKA
          KRESVSKEDLA.RATLVTITNN.GSVARMCAVNE.INRVVFVGN.LRVNTLSMKLLAY.LD.WSKGQLKA
Retrocopy KRESVSKEDLA<RATLVTITNNFGSVARMCAVNEEINRVVFVGNVLRVNTLSMKLLAYTLDFWSKGQLKA

Parental  LFLEHEGYFGAVGALLGLPNFS
          LFLEHEGYFGAV.ALLGLPNFS
Retrocopy LFLEHEGYFGAVSALLGLPNFS

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	0.00 RPM	5.58 RPM
SRP007412_cerebellum	0.00 RPM	7.42 RPM
SRP007412_heart	0.00 RPM	2.32 RPM
SRP007412_kidney	0.00 RPM	3.28 RPM
SRP007412_liver	0.00 RPM	5.39 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2848 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2848 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2848 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011633	4 retrocopies	retro_chof_1188, retro_chof_1391, retro_chof_1837, retro_chof_830,
Callithrix jacchus	ENSCJAG00000015550	1 retrocopy	retro_cjac_2037,
Homo sapiens	ENSG00000120137	1 retrocopy	retro_hsap_779,
Gorilla gorilla	ENSGGOG00000004947	1 retrocopy	retro_ggor_646,
Nomascus leucogenys	ENSNLEG00000004896	5 retrocopies	retro_nleu_1430, retro_nleu_144, retro_nleu_2975, retro_nleu_3058, retro_nleu_3099,
Pongo abelii	ENSPPYG00000016024	1 retrocopy	retro_pabe_2848 ,
Pan troglodytes	ENSPTRG00000017509	1 retrocopy	retro_ptro_608,
Tursiops truncatus	ENSTTRG00000016157	3 retrocopies	retro_ttru_1947, retro_ttru_29, retro_ttru_994,