RetrogeneDB ID: retro_ggor_2082

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:174699227..174701182(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA5
• Ensembl ID: ENSGGOG00000026879
• Aliases: None
• Description: None

Sequence

>retro_ggor_2082
AAGATGAAGCTCTCCCTGGTGGCGGCGATGCTGCTGCTGCTCGGTGAGGCGCGGTTCGAGGACAAGGAGGAGGACGTGGG
CACGGTGGTCTGCGTCGACCTGGGGACCACCTACTGCTGCGTCGGTGTGTTCAAGAATGGCCGCGTGGAGATCACTGCCA
ATAATCAGAGCAAACGCATCGCGCGGTCCTATGTGGCCTTCACTCTTGAAGGGGAATATCTGATCGGCGATGCCGCCACG
AACCAGCTCACCTCCAATCCCAAGAACACGGTCTTTGACGCCAAGTAGCTCATTGGCCGCACGTGGAACGACCTGTCTAT
GCAGCAGGACATCAAGTTCTTGCCGTTCAAGGTAGTTGAAAAGAAAACTAAACCATACGTTCAAGTTGATATTGGAGGTG
GGCAAACAAAGACATTTGCTCCTGAAGAAATTTCTGCCGTGGTTCTCACTAAAATGCAATAAACCGCTGAAGCTTATTTG
AGAAAGAAGTTTACCCATGCAGTTTTTACCTTATCAGCCTATTTCAATGATGCCCAATGCCAAGCAACCAAAGACATTGG
AACTATTGCTGAGCTAAATGTTATGAGGATCATTAACGAGCCTATGGCAGCTGCTATTGGTTATGGCCTGGATAAGAGGG
AGGGGGAGAAGACATCCTGTTGTTCCACCTGGGTGGCAGAACCTTCAATGCGTCTCTTTTCACCATTGACAATGGTGTCT
TCGGAGTCGTGGCCACTAATGGAGATACTCATCTGGGTGCAGAAGACTATGACCAGCGTGTCATGGAACATTTCATCAAG
TTGTACAAAAAGAAGACTGACAAAGATGTCAGGAAAGACGATAGGGCTGTGCAGAAACTACAGCTAGAGGTAGAAAAGGC
CAGATGGGCCCTGTCTCCTCAACATCAAGCAAGAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGACCC
TGACTCGGGCCAAATTTTAAGAGCTAAACATGGATCTGTTCCGGTCTACTATGAGGCCTGTCCAGAAAGTGTTGGAAAAT
TCTGACTTGAAGAATTCTGATATTGATGATGTTGTTCTTGGTGGCTGTACTCGAATTCCAAAGATTCAGCAACTGGTTAA
AAAGTCCTTCAATGGCAAGGAGTCCTCCCATGGCATAAACCCAGATGAAGCTGTAGTGCATGGTGCTGCTGTCCAGGCTG
GAGTGCTCTCTGGTGATCAAGATACAGGTGACCTGGTACTGCTTGATGTATGTCCCCTTACATTTGGTATTGAAACTGTG
GGAGGTGTCATGATCAAACTGATTCCAAGGAACACAGTGGTGCCTACCAAGAAGTCTCATATCTTTTCTATAGCTTCTGA
TAATCAACCAACTGTCATAATCAAGGTCTATGAGGATGAACGACCCCTGACAAAAGACATTCATCTTCTGGGTACATTTG
ATCTGACTGGAATTCCTCCTGCTCCTCGTGGGGTCCCACAGATTGAAGTCACCTTTGAGATAGATGTGAATGGTATTCTT
CGAGTGACAGCTGAAGACAAGGGTACAGGGAACAAAAATAAGGTCACAATTACCAATGACCAGAATCACCTGACACCTGA
AGAAATCAAAAGGATGGTTAATGATGCTGAGAAGTTTGCTGAGGAAGACACAAAGCTCAAGGAGTGCATTGATACTACAA
ATGAGCTGGAAAGCTATGGCTATTCTCTAAAGAATCAGATTGGAGATAAAGAAAAGCTGGGAGGTAAACTTTCCTCTGAA
GATAAGGAGACCATGGGAAAAAGCTGTAGAAGAAAAGATTGAATGGCTGGAAAGCCACCAAGCTGCTGACATTGAAGACT
TCGAAGCTAACAAGAAGGAACTGGAAGAAATTGTTCAGCCACTTATCAGCAAACTCTATGGAAGTGCAGGCCCTCCCCCA
GCCACGAAGAGGATACGGCAGAAAAAGATGAGTTG

Alignment

ORF - retro_ggor_2082 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.32 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KMKLSLVAAMLLLLSAARAEEEDKKEDVGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFT
          KMKLSLVAAMLLLL..AR.E..DK.EDVGTVV..DLGTTY.CVGVFKNGRVEI.AN.Q..RI..SYVAFT
Retrocopy KMKLSLVAAMLLLLGEARFE--DKEEDVGTVVCVDLGTTYCCVGVFKNGRVEITANNQSKRIARSYVAFT

Parental  PEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKT
          .EGE.LIGDAA.NQLTSNP.NTVFDAK.LIGRTWND.S.QQDIKFLPFKVVEKKTKPY.QVDIGGGQTKT
Retrocopy LEGEYLIGDAATNQLTSNPKNTVFDAK*LIGRTWNDLSMQQDIKFLPFKVVEKKTKPYVQVDIGGGQTKT

Parental  FAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAY
          FAPEEISA.VLTKM..TAEAYL.KK.THAV.T..AYFNDAQ.QATKD.GTIA.LNVMRIINEP.AAAI.Y
Retrocopy FAPEEISAVVLTKMQ*TAEAYLRKKFTHAVFTLSAYFNDAQCQATKDIGTIAELNVMRIINEPMAAAIGY

Parental  GLDKREGEK-NILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDV
          GLDKREGEK..IL.F.LGG.TF..SL.TIDNGVF.VVATNGDTHLG.ED.DQRVMEHFIKLYKKKT.KDV
Retrocopy GLDKREGEK<DILLFHLGGRTFNASLFTIDNGVFGVVATNGDTHLGAEDYDQRVMEHFIKLYKKKTDKDV

Parental  RKDNRAVQKLRREVEKAKRALSSQHQARIEIESFYEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLED
          RKD.RAVQKL..EVEKA..ALS.QHQARIEIESFYEGEDFSETLTRAKF.ELNMDLFRSTM.PVQKVLE.
Retrocopy RKDDRAVQKLQLEVEKARWALSPQHQARIEIESFYEGEDFSETLTRAKF*ELNMDLFRSTMRPVQKVLEN

Parental  SDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGDLVLLD
          SDLK.SDID..VL.GG.TRIPKIQQLVK..FNGKE.S.GINPDEAV..GAAVQAGVLSGDQDTGDLVLLD
Retrocopy SDLKNSDIDDVVL-GGCTRIPKIQQLVKKSFNGKESSHGINPDEAVVHGAAVQAGVLSGDQDTGDLVLLD

Parental  VCPLTLGIETVGGVMTKLIPRNTVVPTKKSQIFSTASDNQPTVTIKVYEGERPLTKDNHLLGTFDLTGIP
          VCPLT.GIETVGGVM.KLIPRNTVVPTKKS.IFS.ASDNQPTV.IKVYE.ERPLTKD.HLLGTFDLTGIP
Retrocopy VCPLTFGIETVGGVMIKLIPRNTVVPTKKSHIFSIASDNQPTVIIKVYEDERPLTKDIHLLGTFDLTGIP

Parental  PAPRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNKITITNDQNRLTPEEIERMVNDAEKFAEEDKKLKER
          PAPRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNK.TITNDQN.LTPEEI.RMVNDAEKFAEED.KLKE.
Retrocopy PAPRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNKVTITNDQNHLTPEEIKRMVNDAEKFAEEDTKLKEC

Parental  IDTRNELESYAYSLKNQIGDKEKLGGKLSSEDKETM-EKAVEEKIEWLESHQDADIEDFKAKKKELEEIV
          IDT.NELESY.YSLKNQIGDKEKLGGKLSSEDKETM.EKAVEEKIEWLESHQ.ADIEDF.A.KKELEEIV
Retrocopy IDTTNELESYGYSLKNQIGDKEKLGGKLSSEDKETM>EKAVEEKIEWLESHQAADIEDFEANKKELEEIV

Parental  QPIISKLYGSAGPP-PTGEEDTAEKDEL
          QP.ISKLYGSAGPP.P..EEDTAEKDEL
Retrocopy QPLISKLYGSAGPP<PSHEEDTAEKDEL

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	0.14 RPM	127.27 RPM
SRP007412_cerebellum	0.04 RPM	88.88 RPM
SRP007412_heart	0.00 RPM	72.80 RPM
SRP007412_kidney	0.08 RPM	410.81 RPM
SRP007412_liver	0.03 RPM	288.71 RPM
SRP007412_testis	0.10 RPM	419.06 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2082 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2082 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3005
Pan troglodytes	retro_ptro_2033
Pongo abelii	retro_pabe_2491
Callithrix jacchus	retro_cjac_2221

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 23 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	ENSGGOG00000008381	8 retrocopies	retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
Gorilla gorilla	ENSGGOG00000014154	1 retrocopy	retro_ggor_1747,
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,
Ictidomys tridecemlineatus	ENSSTOG00000011243	4 retrocopies	retro_itri_1686, retro_itri_1687, retro_itri_1689, retro_itri_1879,