RetrogeneDB ID: retro_cjac_2221

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:27453626..27454836(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA5
• Ensembl ID: ENSCJAG00000006880
• Aliases: None
• Description: heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) [Source:HGNC Symbol;Acc:5238]

Sequence

>retro_cjac_2221
GATATACCCCTGGGTGCAGAAGACTTTGACCAGTGTGTCATGGAACACTTCATCAAGCTGTACAAAAGGAAGACTGCAAA
GATGTCAGGAAAGATAACAGAGCTGTGCAGAAACTCTGGGGAGAGGCAGAAAAGGCCAAACAGGCACTGTAGTCTCAACA
TCAAACAAGAAGTGAAACTGAGTCGTTCTATGAAGGAGCAGACTTTTCTGAGACCCTGACTCAGGCCAAATTTGAAGAGC
TAAACATGGATCTGTTCCAGTCTACTATGAAGCCTGTCTAGAAAGTGTTGGAAGATTTTGATTTGAGGAAGTCTCATATT
GATGAAATTGTTCTTGTTAGTGGCTGTACTCAAATCCCAAATATTCAGCAAATGGTTAAAGAGTTATTCAATGGCAAGGA
GCCATCCCATGGTATAAACTCAGATGAAGCTGTAGCATATGGTGCTGCTGTCCAGGATGGTGTGCTCTCTGGTGTTCAAG
ATATAGGTGACCTGGTACTGCTTGATGTATGTTCCTTTACACTTGGTATTGAAAGTGTCGAGGTGTCATGACCAAACTGA
TTCTAAGGAGCAAAGTGGTGGCCACCAAGAGGTCTCATATATTTTCTACAGCTTCTGATAATCAACCAACTGTTATAATC
AAGGTCTTTGAAGCTGTACAATCCCATAAAAGACAATTATCTTCTGGCTCCATCTGTTCTGACAGAAATTCCTCCTGCTC
CTTGTGGGGTCTCACATATTGAAATCACCTTCAAGATAAATGTGACTGGTATTCTTTGAGTAACAGCTGAAGACAAGGGT
ACAGGGAACAAAAATAAGATCTGAATTACCAATGACTAGAATCACGTGACACCTAAGAAATCGAAAGGATGGTTAAGGAT
CCTGAGAAGTTTTCTGAGAAAGACAAAAAGCTCAAGGAGCATATTGATACTAGAAATGAGTTGCAAATTTATGCCTATTC
TCTAAAGAATCAGATTGGAGATAAAGAAAAATCTAGGAGGTAAACTTTCCTCTGAAGATAAGGAGACCATAGAAAAGACT
GTGGAAGAAAAGAATGAATGGCTGGAAAGCCACCAAAATGCTGACATTGAAGACTTCAAAGATAAAAAGGAGGAACTGAG
GGAAACTGTTCAGCCAATTATCAGCAACTGTAAGGATGTACAGGCCCTCCCCCAACTGGCAAAGAGGATACAGCAGAAAA
AGATGAGTTG

Alignment

ORF - retro_cjac_2221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.13 %
• Parental protein coverage: 61.83 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  DTHLGGEDFDQRVMEHFIKLYKKKTG-KDVRKDNRAVQKLRREVEKAKRALSSQHQARIEIESFYEGEDF
          D..LG.EDFDQ.VMEHFIKLYK.KT..KDVRKDNRAVQKL..E.EKAK.AL.SQHQ.R.E.ESFYEG.DF
Retrocopy DIPLGAEDFDQCVMEHFIKLYKRKTA<KDVRKDNRAVQKLWGEAEKAKQAL*SQHQTRSETESFYEGADF

Parental  SETLTRAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGI
          SETLT.AKFEELNMDLF.STMKPV.KVLED.DL.KS.IDEIVLV.G.T.IP.IQQ.VKE.FNGKEPS.GI
Retrocopy SETLTQAKFEELNMDLFQSTMKPV*KVLEDFDLRKSHIDEIVLVSGCTQIPNIQQMVKELFNGKEPSHGI

Parental  NPDEAVAYGAAVQAGVLSGDQDTGDLVLLDVCPLTLGIETV-GGVMTKLIPRNTVVPTKKSQIFSTASDN
          N.DEAVAYGAAVQ.GVLSG.QD.GDLVLLDVC..TLGIE.V..GVMTKLI.R..VV.TK.S.IFSTASDN
Retrocopy NSDEAVAYGAAVQDGVLSGVQDIGDLVLLDVCSFTLGIESV<RGVMTKLILRSKVVATKRSHIFSTASDN

Parental  QPTVTIKVYEGER-PLTKDNHLLGTFDLTGIPPAPRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNKITI
          QPTV.IKV.E....P..KDN.LL....LT.IPPAP.GV..IE.TF.I.V.GIL.VTAEDKGTGNKNKI.I
Retrocopy QPTVIIKVFEAVQ>PI-KDNYLLAPSVLTEIPPAPCGVSHIEITFKINVTGIL*VTAEDKGTGNKNKI*I

Parental  TNDQNRLTPE-EIERMVNDAEKFAEEDKKLKERIDTRNELESYAYSLKNQIGDKEK-LGGKLSSEDKETM
          TND.N..TP..EIERMV.D.EKF.E.DKKLKE.IDTRNEL..YAYSLKNQIGDKEK.LGGKLSSEDKET.
Retrocopy TND*NHVTPK<EIERMVKDPEKFSEKDKKLKEHIDTRNELQIYAYSLKNQIGDKEK>LGGKLSSEDKETI

Parental  EKAVEEKIEWLESHQDADIEDFKAKKKELEEVVQPIIS-KLYGSAGPPPTGEEDTAEKDEL
          EK.VEEK.EWLESHQ.ADIEDFK.KK.EL.E.VQPIIS..L.G..GPPPTG.EDTAEKDEL
Retrocopy EKTVEEKNEWLESHQNADIEDFKDKKEELRETVQPIIS<QL*GCTGPPPTGKEDTAEKDEL

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
SRP051959_colon	0.02 RPM	243.60 RPM
SRP051959_heart	0.02 RPM	97.58 RPM
SRP051959_kidney	0.02 RPM	120.07 RPM
SRP051959_liver	0.00 RPM	342.76 RPM
SRP051959_lung	0.28 RPM	115.73 RPM
SRP051959_lymph_node	0.02 RPM	134.56 RPM
SRP051959_skeletal_muscle	0.00 RPM	111.16 RPM
SRP051959_spleen	0.00 RPM	254.43 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2221 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2221 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2221 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3005
Pan troglodytes	retro_ptro_2033
Gorilla gorilla	retro_ggor_2082
Pongo abelii	retro_pabe_2491

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006880	1 retrocopy	retro_cjac_2221 ,
Callithrix jacchus	ENSCJAG00000007648	5 retrocopies	retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
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,
Ictidomys tridecemlineatus	ENSSTOG00000011243	4 retrocopies	retro_itri_1686, retro_itri_1687, retro_itri_1689, retro_itri_1879,