RetrogeneDB ID: retro_ptro_2109

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:168470125..168471629(-)
• Located in intron of: ENSPTRG00000016575

Retrocopy information

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

Parental gene information

• Parental gene symbol: HADHA
• Ensembl ID: ENSPTRG00000011732
• Aliases: None
• Description: None

Sequence

>retro_ptro_2109
GTGGATCCTGCCATTTTATGCCACTACAGAATAGCAACAAAAGACAGAAAAACAGTATTCGGTGCTCCTGAAGTCTTGCT
GGGGATCTTACCAGGAGCAGGAGGCACACAAAGGCTGCCCAAAATGGTGGGTGTGCCTGCTGCTTTTGACATGATGCTGA
CTGCTAGAAACATGCGTGCAGACAGGGCAAAGAAAATGGGACTGGTTGACCAATTGGTGGAATCTCTGGGACCAGGACTA
AAACTTCCAGAGGAATGGACAATCAAATACCTAGAAGAAGTCGCAATTACTTTCCCAAAGGACTAGCTGATAAGAAGATC
TCTCCAAAGAGAAACAAGGGATTAGTGGAAAAATTAACAGCGTATGCCATGACTATTCCATTTGTCAGGCAACAGATTTA
CAAAAAAGTGGAAGAAAAAGTGTGAAAGCGGACTAAAGGGCTTTATCCCACACCTCTGAAAATAATTGATGTGGTAAAGA
CTGGAATTGAGCAAGGGAGTGATGCTGGTTATCTCTCTGAATCTCAGAAATTCGGAGAGCTTGCAATGACCAAAGAATCA
AAGGCCTTGATGGGACTCTACCATGGTCAGGTCCTGTGCAAGAAGAATACATCTGGAGCTCCACAGAAGGATGTTAAGCA
TCTGGCTATTCCTGGTGCAGGGATGATGGGAGCAGGCATTGCCCAAGTCTCCGTGGATAAGGGGCGAAAGACTATACTTA
AAGATGCCACACTCACTGGGTTAGGGTGAGGACAGCAACAAGTGTTCAAAGGATTGAATGACAAAGTAGAGAAGAAAGCT
CTAACGTCATTTGAAAGGGATTCCATCTTCAGCAACTTGACTGGGAAGCTTGATTACCAAGGTTTTGAAAGACGGACATG
GTGATGGATGCTGTGTTCGAGGACCTTAGTTTTAAGCATAGAGTGCTAAAGGGAGTAGAAGCAGTGATTCCAGATCACTA
TGTCTTTGCCAGTAACACATCTCCTCTCCCAATCAGTGAAATCGCTGCTGTCAGCAAAAGACCTGAGAAGGTGATTGGTA
GGCACTACTTCTCTCCCGCAGACAAGATGCAGCTGCTGGAGATGATCACAACCGAGAAGACTTCCAAAGACACCAGTGCT
TCAACTGTAGCAATCGGTCTCAAGCAGGGGAAGGTCATCATTGTGGTTAAGGATGGACCTGGCTTCTATACCACCAGGTG
TCTTGCACCCATGATGTCTGAAGTCATCCGAATCCTCCAGGAAGGAGTTGACCCGAAGAAGCTGGATTCCCTGACCACAA
GCCTTGGCCTTCCTGTGGGTGCCGCCACACTGGTGGATGAAGTTGGCGTGGATGTAGCGAAACATGTGGCCAAAGATCTG
GGCAAAGCCTTTGGGGAGCGGTTTGGAGGTGGAAACCCAGAACTACTGACATAGATGGTGTCCAAGGGCTTCCTAGGTCG
CAAGTCTGGGGAGGGCTTTTCCATCTATCAGGAGAGTGTGAAGAATAAGAATTTGAATTCTGAA

Alignment

ORF - retro_ptro_2109 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.29 %
• Parental protein coverage: 65.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LEVAISCQYRIATKDRKTVLGTPEVLLGALPGAGGTQRLPKMVGVPAALDMMLTGRSIRADRAKKMGLVD
          ...AI.C.YRIATKDRKTV.G.PEVLLG.LPGAGGTQRLPKMVGVPAA.DMMLT.R..RADRAKKMGLVD
Retrocopy VDPAILCHYRIATKDRKTVFGAPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTARNMRADRAKKMGLVD

Parental  QLVEPLGPGLKPPEERTIEYLEEVAITFAK-GLADKKISPKRDKGLVEKLTAYAMTIPFVRQQVYKKVEE
          QLVE.LGPGLK.PEE.TI.YLEEVAITF.K.GLADKKISPKR.KGLVEKLTAYAMTIPFVRQQ.YKKVEE
Retrocopy QLVESLGPGLKLPEEWTIKYLEEVAITFPK<GLADKKISPKRNKGLVEKLTAYAMTIPFVRQQIYKKVEE

Parental  KVRKQTKGLYPAPLKIIDVVKTGIEQGSDAGYLSESQKFGELVMTKESKALMGLYHGQVLCKKNKFGAPQ
          KV.K.TKGLYP.PLKIIDVVKTGIEQGSDAGYLSESQKFGEL.MTKESKALMGLYHGQVLCKKN..GAPQ
Retrocopy KV*KRTKGLYPTPLKIIDVVKTGIEQGSDAGYLSESQKFGELAMTKESKALMGLYHGQVLCKKNTSGAPQ

Parental  KDVKHLAILGAGLMGAGIAQVSVDKGLKTILKDATLTALDRGQQQVFKGLNDKVKKKALTSFERDSIFSN
          KDVKHLAI.GAG.MGAGIAQVSVDKG.KTILKDATLT.L..GQQQVFKGLNDKV.KKALTSFERDSIFSN
Retrocopy KDVKHLAIPGAGMMGAGIAQVSVDKGRKTILKDATLTGLG*GQQQVFKGLNDKVEKKALTSFERDSIFSN

Parental  LTGQLDYQGFE-KADMVIEAVFEDLSLKHRVLKEVEAVIPDHCIFASNTSALPISEIAAVSKRPEKVIGM
          LTG.LDYQGFE.K.DMV..AVFEDLS.KHRVLK.VEAVIPDH..FASNTS.LPISEIAAVSKRPEKVIG.
Retrocopy LTGKLDYQGFE<KTDMVMDAVFEDLSFKHRVLKGVEAVIPDHYVFASNTSPLPISEIAAVSKRPEKVIGR

Parental  HYFSPVDKMQLLEIITTEKTSKDTSASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVD
          HYFSP.DKMQLLE.ITTEKTSKDTSAS.VA.GLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVD
Retrocopy HYFSPADKMQLLEMITTEKTSKDTSASTVAIGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVD

Parental  PKKLDSLTTSFGFPVGAATLVDEVGVDVAKHVAEDLGKVFGERFGGGNPELLTQMVSKGFLGRKSGKGFY
          PKKLDSLTTS.G.PVGAATLVDEVGVDVAKHVA.DLGK.FGERFGGGNPELLT.MVSKGFLGRKSG.GF.
Retrocopy PKKLDSLTTSLGLPVGAATLVDEVGVDVAKHVAKDLGKAFGERFGGGNPELLT*MVSKGFLGRKSGEGFS

Parental  IYQEGVKRKDLNSD
          IYQE.VK.K.LNS.
Retrocopy IYQESVKNKNLNSE

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	0.20 RPM	74.68 RPM
SRP007412_cerebellum	0.36 RPM	91.70 RPM
SRP007412_heart	0.15 RPM	327.92 RPM
SRP007412_kidney	0.08 RPM	220.98 RPM
SRP007412_liver	0.13 RPM	126.62 RPM
SRP007412_testis	0.00 RPM	184.53 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2109 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2109 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2109 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2576
Macaca mulatta	retro_mmul_1987

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006972	1 retrocopy	retro_dnov_1863,
Homo sapiens	ENSG00000084754	1 retrocopy	retro_hsap_958,
Gorilla gorilla	ENSGGOG00000004918	1 retrocopy	retro_ggor_772,
Macaca mulatta	ENSMMUG00000004380	2 retrocopies	retro_mmul_1987, retro_mmul_787,
Mustela putorius furo	ENSMPUG00000008546	1 retrocopy	retro_mputfur_705,
Nomascus leucogenys	ENSNLEG00000001616	2 retrocopies	retro_nleu_1588, retro_nleu_772,
Pongo abelii	ENSPPYG00000012583	2 retrocopies	retro_pabe_2576, retro_pabe_817,
Pan troglodytes	ENSPTRG00000011732	2 retrocopies	retro_ptro_2109 , retro_ptro_664,
Pan troglodytes	ENSPTRG00000016351	1 retrocopy	retro_ptro_1058,
Ictidomys tridecemlineatus	ENSSTOG00000001593	1 retrocopy	retro_itri_681,