RetrogeneDB ID: retro_ptro_2033

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:167297003..167298954(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA5
• Ensembl ID: ENSPTRG00000000563
• Aliases: None
• Description: None

Sequence

>retro_ptro_2033
ATGAAGCTCTCCCTGGTGGCGGCGATGCTGCTGCTACTCGGTGAGGCGCGGTTCGAGGACAAGGAGGAGGACGTGGGCAC
GGTGGTCTGCGTCGACCTGGGGACCACCTACTGCTGCGTCGGTGTGTTCAAGACCGGCTGCGTGGAGATCACCGCCAACA
ATCAGAGCAAACGCATCACGCGGTCCTATGTGCCCTTCACTCTTGAAGGGGAATATCTGATCGGCGATGCCGCCACGAAC
CAGCTCACCTCCAATCCCAAGAACACGGTCTTTGACGCCAAGTGGCTCATCGGCCGCACGTGGAACGACCTGTCTATGCA
GCAGGACATCAAGTTCTTGCCGTTCAAGGTAGTTGAAAAGAAAACTAAACCATACGTTCAAGTTGATATTGGAGGTGGGC
AAACAAAGACATTTGCTCCTGAAGAAATTTCTGCCATGGTTCTCACTAAAATGCAATAAACCGCTGAGGCTTATTTGAGA
AAGAAGTTTACCCATGCAGTTTTTACCTTACCAGCCTATTTCAATGATGCCCAATGCCAAGCAACCAAAGACATTGGAAC
TATTGCTGAGCTAAATGTTATGAGGATCATTAACGAGCCTATGGCAGCTGCTATTGGTTATGGCCTGGATAAGAGGGAGG
GGGAGAAGACATCCTGTTGTTCCACCTGGGTGGCAGAACCTTCAATGCGTCTCCTCTCACCATTGACAATGGTGTCTTCG
GAGTCGTGGCCACTAATGGAGATACTCATCTGGGTGCAGAAGACTATGACCAGCGTGTCATGGAACATTTCATCAAGTTG
TACAAAAAGAAGACTGACAAAGATGTCAGGAAAGACGATAGGGCTGTGCAGAAACTCCAGCTAGAGGCAGAAAAGGCCAG
ATGGGCCCTGTCTCCTCAACATCAAGCAAGAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGACCCTGA
CTCGGGCCAAATTTTAAGAGCTAATCATGGATCTGTTCCGGTCTACTATGAGGCCTGTCCAGAAAGTGTTGGAAAATTCT
GATTTGAAGAATTCTGATATTGATGATGTTGTTCTTGGTGGCTCTACTCGAATTCCAAAGATTCAGCAACTGGTTAAAAA
GTCCTTCAATGGCAAGGAGTCCTCCCATGGCATAAACCCAGATGAAGCTGTAGTGCATGGTGCTGCTGTCCAGGCTGGAG
TGCTCTCTGGTGATCAAGATACAGGTGACCTGGTACTGCTTGATGTATGTCCCCTTACATTTGGTATTGAAACTGTGGGA
GGTGTCATGATCAAACTGATTCCAAGGAACACAGTGGTGCCTACCAAGAAGTCTCATATCTTTTCTATAGCTTCTGATAA
TCAACCAACTGTCATAATCAAGGTCTATGAGGATGAACGACCCCTGACAAAAGACATTCATCTTCTGGGTACATTTGATC
TGACTGGAATTCCTCCTGCTCCTCGTGGGGTCCCACAGATTGAAGTCACCTTTAAGATAGATGTGAATGGTATTCTTCGA
GTGACAGCTGAAGACAAGGGTACAGGGAACAAAAATAAGATCACAATTACCAATGACCAGAATCACCTGACACCTGAAGA
AATCAAAAGGATGGTTAATGATGCTGAGAAGTTTGCTGAGGAAGACACAAAGCTCAAGGAGTGCATTGATACTACAAATG
AGCTGGAAAGCTATGGCTATTCTCTAAAGAATCAGATTGGAGATAAAGAAAAGCTGGGAGGTAAACTTTCCTCTGAAGAT
AAGGAGACCATGGAAAAAGCTGTAGAAGAAAAGATTGAATGGCTGGAAAGCCACCAAGCTGCTGACATTGAAGACTTCGA
AGCTAACAAGAAGGAACTGGAAGAAATTGTTCAGCCACTTATCAGCAAACTCTATGGAAGTGCAGGCCCTCTCCCAGCCA
CGAGGAGGATATGGCAGAAAAAGATGAGTTG

Alignment

ORF - retro_ptro_2033 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.98 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKLSLVAAMLLLLSAARAEEEDKKEDVGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTP
          MKLSLVAAMLLLL..AR.E..DK.EDVGTVV..DLGTTY.CVGVFK.G.VEI.AN.Q..RIT.SYV.FT.
Retrocopy MKLSLVAAMLLLLGEARFE--DKEEDVGTVVCVDLGTTYCCVGVFKTGCVEITANNQSKRITRSYVPFTL

Parental  EGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKTF
          EGE.LIGDAA.NQLTSNP.NTVFDAK.LIGRTWND.S.QQDIKFLPFKVVEKKTKPY.QVDIGGGQTKTF
Retrocopy EGEYLIGDAATNQLTSNPKNTVFDAKWLIGRTWNDLSMQQDIKFLPFKVVEKKTKPYVQVDIGGGQTKTF

Parental  APEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYG
          APEEISAMVLTKM..TAEAYL.KK.THAV.T.PAYFNDAQ.QATKD.GTIA.LNVMRIINEP.AAAI.YG
Retrocopy APEEISAMVLTKMQ*TAEAYLRKKFTHAVFTLPAYFNDAQCQATKDIGTIAELNVMRIINEPMAAAIGYG

Parental  LDKREGEK-NILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVR
          LDKREGEK..IL.F.LGG.TF..S.LTIDNGVF.VVATNGDTHLG.ED.DQRVMEHFIKLYKKKT.KDVR
Retrocopy LDKREGEK<DILLFHLGGRTFNASPLTIDNGVFGVVATNGDTHLGAEDYDQRVMEHFIKLYKKKTDKDVR

Parental  KDNRAVQKLRREVEKAKRALSSQHQARIEIESFYEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDS
          KD.RAVQKL..E.EKA..ALS.QHQARIEIESFYEGEDFSETLTRAKF.EL.MDLFRSTM.PVQKVLE.S
Retrocopy KDDRAVQKLQLEAEKARWALSPQHQARIEIESFYEGEDFSETLTRAKF*ELIMDLFRSTMRPVQKVLENS

Parental  DLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGDLVLLDV
          DLK.SDID..VL.GGSTRIPKIQQLVK..FNGKE.S.GINPDEAV..GAAVQAGVLSGDQDTGDLVLLDV
Retrocopy DLKNSDIDDVVL-GGSTRIPKIQQLVKKSFNGKESSHGINPDEAVVHGAAVQAGVLSGDQDTGDLVLLDV

Parental  CPLTLGIETVGGVMTKLIPRNTVVPTKKSQIFSTASDNQPTVTIKVYEGERPLTKDNHLLGTFDLTGIPP
          CPLT.GIETVGGVM.KLIPRNTVVPTKKS.IFS.ASDNQPTV.IKVYE.ERPLTKD.HLLGTFDLTGIPP
Retrocopy CPLTFGIETVGGVMIKLIPRNTVVPTKKSHIFSIASDNQPTVIIKVYEDERPLTKDIHLLGTFDLTGIPP

Parental  APRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNKITITNDQNRLTPEEIERMVNDAEKFAEEDKKLKERI
          APRGVPQIEVTF.IDVNGILRVTAEDKGTGNKNKITITNDQN.LTPEEI.RMVNDAEKFAEED.KLKE.I
Retrocopy APRGVPQIEVTFKIDVNGILRVTAEDKGTGNKNKITITNDQNHLTPEEIKRMVNDAEKFAEEDTKLKECI

Parental  DTRNELESYAYSLKNQIGDKEKLGGKLSSEDKETMEKAVEEKIEWLESHQDADIEDFKAKKKELEEIVQP
          DT.NELESY.YSLKNQIGDKEKLGGKLSSEDKETMEKAVEEKIEWLESHQ.ADIEDF.A.KKELEEIVQP
Retrocopy DTTNELESYGYSLKNQIGDKEKLGGKLSSEDKETMEKAVEEKIEWLESHQAADIEDFEANKKELEEIVQP

Parental  IISKLYGSAG-PPPTGEEDTAEKDEL
          .ISKLYGSAG.P.P..EED.AEKDEL
Retrocopy LISKLYGSAG<PSPSHEEDMAEKDEL

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	0.05 RPM	122.55 RPM
SRP007412_cerebellum	0.07 RPM	142.68 RPM
SRP007412_heart	0.03 RPM	166.63 RPM
SRP007412_kidney	0.08 RPM	321.59 RPM
SRP007412_liver	0.26 RPM	1051.75 RPM
SRP007412_testis	0.32 RPM	531.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2033 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2033 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2033 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3005
Gorilla gorilla	retro_ggor_2082
Pongo abelii	retro_pabe_2491
Callithrix jacchus	retro_cjac_2221

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006880	1 retrocopy	retro_cjac_2221,
Homo sapiens	ENSG00000044574	1 retrocopy	retro_hsap_3005,
Gallus gallus	ENSGALG00000001000	1 retrocopy	retro_ggal_21,
Gorilla gorilla	ENSGGOG00000026879	1 retrocopy	retro_ggor_2082,
Macropus eugenii	ENSMEUG00000016702	1 retrocopy	retro_meug_522,
Mus musculus	ENSMUSG00000026864	1 retrocopy	retro_mmus_1299,
Nomascus leucogenys	ENSNLEG00000017348	1 retrocopy	retro_nleu_751,
Otolemur garnettii	ENSOGAG00000006786	1 retrocopy	retro_ogar_2901,
Pongo abelii	ENSPPYG00000019609	1 retrocopy	retro_pabe_2491,
Pan troglodytes	ENSPTRG00000000563	1 retrocopy	retro_ptro_2033 ,
Pan troglodytes	ENSPTRG00000004404	5 retrocopies	retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Pan troglodytes	ENSPTRG00000017290	1 retrocopy	retro_ptro_1680,
Ictidomys tridecemlineatus	ENSSTOG00000011243	4 retrocopies	retro_itri_1686, retro_itri_1687, retro_itri_1689, retro_itri_1879,