RetrogeneDB ID: retro_ptro_608

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 11:49808564..49809672(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PANK3
• Ensembl ID: ENSPTRG00000017509
• Aliases: None
• Description: None

Sequence

>retro_ptro_608
ATGAAGATCAAAGATGGCAAGAAACCCTCTTTCCCATGGTTTGGCATGGACATTGGGGGAACTCTAGTAAACCTCTCGTA
CTTTGAACCTATTGCTATCACAGCAGAGGAAGAACAAAAAGAAGTTGAGAGTTTAAAAAGTATTCGAAAATATTTGATTT
CTAATGTAGCATGTGGATCCACCGGCATTAGGGATGTACACCTTGAACTGAAAGATTTAACACTTTTTGGCCGAAGAGGG
AACCTGCACTTTACAGGTTTCCAACCCAGGACCTGCCTACTTTTATCCAAATGGGAAGAGATAAAAACTTCTCAACATTG
CAAATGGTGCTATGTGCTACAGGAGGTGGTGCCTACAAGTTTGAAAAAGATTTTCGCACAATTGGAAACCTCCACCTGCA
CAAACTGGATGAACTTGACTGCCTTGTAAAGGGCTTGCTGTATATAGACTGTTGGTTTCAATGGACATGCGGAGTGCTAT
TATTTAGCTAATGCCTCAGAACCTCAGCAATGCCAAAAGATGCCTTTTAACCTGGATGTTCCCTACCCACTGCTTGTAGT
GAACATTGGCTCAGGAGTCAGTATTTTAGCAGTCCATTCCAAAGACATCTATAAACGAATGACTGGGACAAGCCTTGGGG
AGGGTACCTTTCTGGGTTTATGCAGTTTATTGACTGGCTGTGAAAGTTTTGAAGAGGCTCTTGAAATGGCATTCCAAAGG
TGACAGCACACAAGCTGACAAGCTGACCCATGATATTTATGGAGGAGATCATGAAAGATTTGGTTTGCCAGGTTGAACTG
TAGCATCTAGTTTTAGGAATATGATTTATAAGGAGAAGCGAGAATCTGTTAGTAAAGAAGATCTGGCAAGAGCTACTTTA
GTTACTATCACCAATAACTTCGGTTCTGTGGCACGAAAGTGTGCTGTTAATGAGAAAATCAACAGAGTTGTCTTTGTTGG
AAACGTTTTATGTGTCAATACCCTCTCAGTGAAACTTTTGGCATATGCACCGGATCTTTCGTCAAAAGGTCAACTGAAAG
CATTGTTTCTAGAACATGAGGGATACTTTGGAGCAGTTAATGCACTTCTTGGGCTGCCAAATTTCAGC

Alignment

ORF - retro_ptro_608 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.3 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MKIKDAKKPSFPWFGMDIGGTLVKLSYFEPIDITAEEEQEEVESLKSIRKYLTSNVAYGSTGIRDVHLEL
          MKIKD.KKPSFPWFGMDIGGTLV.LSYFEPI.ITAEEEQ.EVESLKSIRKYL.SNVA.GSTGIRDVHLEL
Retrocopy MKIKDGKKPSFPWFGMDIGGTLVNLSYFEPIAITAEEEQKEVESLKSIRKYLISNVACGSTGIRDVHLEL

Parental  KDLTLFGRRGNLHFI-RFPTQDLPTFIQMGRDKNFSTLQTVLCATGGGAYKFEKDFRTIGNLHLHKLDEL
          KDLTLFGRRGNLHF..RFPTQDLPTFIQMGRDKNFSTLQ.VLCATGGGAYKFEKDFRTIGNLHLHKLDEL
Retrocopy KDLTLFGRRGNLHFT<RFPTQDLPTFIQMGRDKNFSTLQMVLCATGGGAYKFEKDFRTIGNLHLHKLDEL

Parental  DCLV-KGLLY-IDSVSFNGQAECYYFANASEPERCQKMPFNLDDPYPLLVVNIGSGVSILAVHSKDNYKR
          DCLV.KGL...I..V.FNG.AECYY.ANASEP..CQKMPFNLD.PYPLLVVNIGSGVSILAVHSKD.YKR
Retrocopy DCLV<KGLAV<I*TVGFNGHAECYYLANASEPQQCQKMPFNLDVPYPLLVVNIGSGVSILAVHSKDIYKR

Parental  VTGTSLGGGTFLGLCSLLTGCESFEEALEMA-SKGDSTQADKLVRDIYGGDYERFGLPGWAVASSFGNMI
          .TGTSLG.GTFLGLCSLLTGCESFEEALEMA.SKGDSTQADKL..DIYGGD.ERFGLPG..VASSF.NMI
Retrocopy MTGTSLGEGTFLGLCSLLTGCESFEEALEMA>SKGDSTQADKLTHDIYGGDHERFGLPG*TVASSFRNMI

Parental  YKEKRESVSKEDLARATLVTITNNIGSVARMCAVNEKINRVVFVGNFLRVNTLSMKLLAYALDYWSKGQL
          YKEKRESVSKEDLARATLVTITNN.GSVAR.CAVNEKINRVVFVGN.L.VNTLS.KLLAYA.D..SKGQL
Retrocopy YKEKRESVSKEDLARATLVTITNNFGSVARKCAVNEKINRVVFVGNVLCVNTLSVKLLAYAPDLSSKGQL

Parental  KALFLEHEGYFGAVGALLGLPNFS
          KALFLEHEGYFGAV.ALLGLPNFS
Retrocopy KALFLEHEGYFGAVNALLGLPNFS

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	11.87 RPM
SRP007412_cerebellum	0.00 RPM	29.25 RPM
SRP007412_heart	0.00 RPM	13.84 RPM
SRP007412_kidney	0.00 RPM	20.19 RPM
SRP007412_liver	0.00 RPM	18.40 RPM
SRP007412_testis	0.00 RPM	30.25 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_608 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_608 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_608 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_779
Gorilla gorilla	retro_ggor_646

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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,