RetrogeneDB ID: retro_cjac_3306

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:56182258..56184223(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA8
• Ensembl ID: ENSCJAG00000007648
• Aliases: None
• Description: heat shock 70kDa protein 8 [Source:HGNC Symbol;Acc:5241]

Sequence

>retro_cjac_3306
CGGGTCCAGGCCAACACGCCAGCAACCATGTCGAAGGGACCCGCCGTTGGTATTGATCTTGGCACCACCTACTCTTGTGT
GGGTGTTTTCCAGCACGGAAAAGTAGAAATAATTGCCAATGATCAAGGAAACCGAACCACTCCAAGCTATGTCACCTTTA
CGGACACTGAACAATTGATCGGTGATGCCGCAAAGAATCAAGTTGCAATGAACCCCACCAACACGGTTTTTGATGCCAAA
CGTCTGATTGGATGCAGATTTGAAGATGCCATTGTCCAGTCTGATATGAAGCATTGGCCCTTTATGGTAGTGAATGATGC
TGGCAGGCCCAAGGTCCAAGTAGAATACAAGGGAGAGACAAAAAGCTTCTATCCAGAGGAGGTATCCTCTATGGTTCTGA
CAAAGATGAAGGAAATTGCAGAAGCCTACCTTGGGAAGACTGTTACCAATGCTGTGGTCACAGTGCCCGCTTACTTTAAT
GACTCTCAGCGTCAGGCTACCAAAGATGCTGGAACTATTGCTGGTCTCAATGTACTTAGAATTATTAATGAGCCAACTGC
TGCTGCTATTGCTTATGGCTTAGACAAAAAGGTTGGAGCTGAGAGAAACGTGCTGATCTTTGATCTTGGAGGTGGCACTT
TTGATGTGTCAATCCTCACTATTGAGGATGGAATCTTTGAGGTCAAGTCTACAGCTGGAGACACGCACTTGGGTGGAGAA
GATTTTGATAACCGAACGGTCAACCATTTCATTGCTGAGTTCAAGCGCAAGCATAAGAAGGACATAAGTGAGAACAAGAG
AGCTGTAAGACGCCTCTGTACTGCTTGTGAGCGTGCTAAGCGTACTCTCTCTTCTAGCACCCAGGCTAGTATTGAAATCG
ATTCCCTATATAAAGGAATCGACTTCTATACCTCCATTACCCGTGCCTGATTTGAAGAATTGAATGCTGACTTGTTCCGT
GGAACCCTGGACCCCGTAGAGAAGGCCCTTCGAGATGCCAAACTAGACAAGTCTCAAATTCATGATATTGTCCTGGTTGG
TGGTTCTACTCGCATCCCCAAAATTCAGAAGCTTCTCCAAGACTTTTTCAATGGAAAAGAACTGAATAAGAGCATCAACC
CTGATGAAGCTGTTGCTTATGGTGCAGCTGTCCAGGCCGCCATTCTGTCTGGAGATAAGTCTGAAAATGTTCAAGATTTG
CTGCTCTTGGATGTCACTCCTCTTTCCCTTGGCATTGAAACTGCTGGTGGAGTCATGACCATCCTCATCAAGCGTAATAC
TACCATTCCCACCAAGCAGACACAGACCTTCACTACCTATTCCGACAACCAGCCTGGTGTGCTTATTCAGGTTTATGAAG
GTGAGCGTGCCATGACCAAGGATAACAACCTGCTTGGCAAGTTTGAACTTACAGGCATACCTCCTGCACCCCGAGGTGTT
CCTCAGATTGAGGTCACTTTTGACATTGATGCCAATGGCATTCTCAATGTGTCTGCTGTGGACAAGAGTACAGGAAAAGA
GAACAAGATTACTATCACTAATGACAAGGGCTGTTTGAGCAAGGAAGACATTGAACGTATGGTCCAGGGAGCTGAGAAGT
ACAAAGCTGAAGACGAGAAGCAGAGGGACAAAGTGTCATCTAAGAATTCACTTGAATCCTATGCATTTAACATGAAAGCA
ACTGTTGAAGATGAGAAACTTCAAGGCAAGATTAACGATGAGGATAAACAGAAGATTCTGGACAAGTGTAATGAAATTAT
CAACTGGCTTGATAAGAATCAGACTGCCGAGAAGGAAGAATTTGAACATCAGCAAAAAGAGCTGGAGAAAGTCTGCAACC
CCATCATCACCAAGCTGTACCAGAGTGCAGGAGGCATGCCAGGAGGAATGCCTGGAGGATTCCCTGGTGGTGGAGCTCCT
CCCTCTGGTGGTGCTTCCTCAGGGCCCACTATTGAAGAGGTTGAT

Alignment

ORF - retro_cjac_3306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.96 %
• Parental protein coverage: 99.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RQDRNVGSTMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAM
          R...N...TMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYV.FTDTE.LIGDAAKNQVAM
Retrocopy RVQANTPATMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVTFTDTEQLIGDAAKNQVAM

Parental  NPTNTVFDAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIA
          NPTNTVFDAKRLIG.RF.DA.VQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIA
Retrocopy NPTNTVFDAKRLIGCRFEDAIVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIA

Parental  EAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLG
          EAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLG
Retrocopy EAYLGKTVTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLG

Parental  GGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAK
          GGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNR.VNHFIAEFKRKHKKDISENKRAVRRL.TACERAK
Retrocopy GGTFDVSILTIEDGIFEVKSTAGDTHLGGEDFDNRTVNHFIAEFKRKHKKDISENKRAVRRLCTACERAK

Parental  RTLSSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGST
          RTLSSSTQASIEIDSLY.GIDFYTSITRA.FEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGST
Retrocopy RTLSSSTQASIEIDSLYKGIDFYTSITRA*FEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGST

Parental  RIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMT
          RIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMT
Retrocopy RIPKIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMT

Parental  VLIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDID
          .LIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDID
Retrocopy ILIKRNTTIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDID

Parental  ANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKA
          ANGILNVSAVDKSTGKENKITITNDKG.LSKEDIERMVQ.AEKYKAEDEKQRDKVSSKNSLESYAFNMKA
Retrocopy ANGILNVSAVDKSTGKENKITITNDKGCLSKEDIERMVQGAEKYKAEDEKQRDKVSSKNSLESYAFNMKA

Parental  TVEDEKLQGKINDEDKQKILDKCNEIINWLVKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGM
          TVEDEKLQGKINDEDKQKILDKCNEIINWL.KNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGM
Retrocopy TVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGM

Parental  PGGFPGGGAPPSGGASSGPTIEEVD
          PGG..............GPTIEEVD
Retrocopy PGGXXXXXXXXXXXXXXGPTIEEVD

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	66.43 RPM	328.33 RPM
SRP051959_heart	42.99 RPM	200.64 RPM
SRP051959_kidney	67.29 RPM	314.33 RPM
SRP051959_liver	96.15 RPM	456.22 RPM
SRP051959_lung	69.59 RPM	320.55 RPM
SRP051959_lymph_node	88.47 RPM	414.60 RPM
SRP051959_skeletal_muscle	47.67 RPM	227.20 RPM
SRP051959_spleen	80.95 RPM	368.89 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3306 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3306 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3306 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 29 parental genes, and 88 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004884	2 retrocopies	retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca	ENSAMEG00000008425	1 retrocopy	retro_amel_126,
Anas platyrhynchos	ENSAPLG00000010667	1 retrocopy	retro_apla_6,
Bos taurus	ENSBTAG00000013162	1 retrocopy	retro_btau_354,
Canis familiaris	ENSCAFG00000011666	3 retrocopies	retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis	ENSCING00000009665	1 retrocopy	retro_cint_12,
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,
Cavia porcellus	ENSCPOG00000004169	3 retrocopies	retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi	ENSCSAVG00000008588	1 retrocopy	retro_csav_3,
Echinops telfairi	ENSETEG00000010996	1 retrocopy	retro_etel_43,
Ficedula albicollis	ENSFALG00000005812	1 retrocopy	retro_falb_18,
Felis catus	ENSFCAG00000001132	6 retrocopies	retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Gallus gallus	ENSGALG00000006512	1 retrocopy	retro_ggal_8,
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,
Loxodonta africana	ENSLAFG00000030312	4 retrocopies	retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo	ENSMGAG00000001929	1 retrocopy	retro_mgal_9,
Myotis lucifugus	ENSMLUG00000004834	3 retrocopies	retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Monodelphis domestica	ENSMODG00000012958	2 retrocopies	retro_mdom_127, retro_mdom_99,
Mustela putorius furo	ENSMPUG00000005810	9 retrocopies	retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Mus musculus	ENSMUSG00000015656	8 retrocopies	retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Oryctolagus cuniculus	ENSOCUG00000015533	4 retrocopies	retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus	ENSONIG00000004759	1 retrocopy	retro_onil_2,
Pongo abelii	ENSPPYG00000003987	9 retrocopies	retro_pabe_183, retro_pabe_2193, retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pelodiscus sinensis	ENSPSIG00000012450	2 retrocopies	retro_psin_17, retro_psin_5,
Taeniopygia guttata	ENSTGUG00000000491	1 retrocopy	retro_tgut_7,
Takifugu rubripes	ENSTRUG00000005265	1 retrocopy	retro_trub_30,
Tursiops truncatus	ENSTTRG00000011139	6 retrocopies	retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus	ENSXMAG00000001602	1 retrocopy	retro_xmac_20,