RetrogeneDB ID: retro_cjac_3152

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:76278849..76281497(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EHMT2
• Ensembl ID: ENSCJAG00000037618
• Aliases: None
• Description: None

Sequence

>retro_cjac_3152
TCAGGGAATCAGTCAGATAGGAGTGGTTCTAGTGGCCGGCACAAGGCCAAGAAGAAATGGCTAAAAGACAGCCCATGGGT
GAAGTCATCTAGGAAACGGCGCAAGTGGGAGCCTCCAAGGGCCAAGGAGCCATGAGGAGTGAATGGTGTGGGCTCCTCAG
GCCCCAATGAGTATATGGAGGTCCCTCTGGGGTCCCTGGAGCTGCCCAGGGAGGGGACCCTCTCCCCCAACCACTCTGGG
GTGTCCAATGACACATCTTTGCTGGAGACAGAGCGTGGGTTTGAGGAGTTGCCCCTGTGCAGCTGCTGCATGAAGGCACC
CAAGACTGACCACATCAGCGAGAGGGCAGAGCACAAGTACATGGCCATGGAGAGTGTGGATGGAGAGCTGTCGGGCTGCA
AAGCTGCCATCCTCAAGCGGGAGACCGTGAGGCCATCCAGCCACGTGACCCTGATGGTGCTCTGTGAGACCCACCATGCC
CGCATGGTCAAACACCAATGCTGTTCGGGCTGTGGCTACTTCTGCATGGCAGACACCTTCCTGGTGTGCCACCCTGACTT
CTGGATGGCCCACCACTTCCACAAGGCCTGTGTGTCCCAGCTGAATGGGATGGTCTTCTGTCCCCACTGTGGGGAGGATG
CTTCTGAGGCTCAGGAGGTGACCATCCCCCATGGTGATGGGGTGACCACACCAGCTGGCACTGCAGCTCCTGCACCCCCA
CCCCATCCCAGGATGACCCCGGGAGAGCAGGCACTTCCCAGCCCAGCGCCCGGATGCGAGGCCATGGGGAGCCCTGGTGC
CCACCCTGCAATCCCCTGGCCGACACCATCGACAGCTCAGGACCGTCCCTGACACTGCCCAATGGGGGCTGCCTTTCCAC
CGTGGGGCTGCCACTGGGGCCAGGCCAGGAGGCCCTGGAAAAGGCCCTGGCCATCCAGGAGTCAGAGAGGCAGAAGAAGC
TCCGTTTCCATCTTCGGCAGTTGTACCTGCCTGTAAAGCAGGGCAAGCTGCAGAAGGTGATCCTGATGCTGTTGGACAAC
CTGGACCCCAACTTCGAGAGCGACCAGCAGAGCAAGCGTCCGCCCTTGCATGCAGGCGCCCAGAAGGGCTCTGTGGAGAT
CTGCCATGTGCTGCTGCAGGCTGGAGCCAAGATAAATGCAGTGGACAAACAGCAGTGGGTGCCACTGATGGAGGCCATGG
TGAACAACCACCTGGAGGTGGCCCGTTACATGGTGCAGCGTGGCAGCTGCATCTATAGCAAGGAGGTGGATGGTTCCACC
TGCCTCCACCACGCAGCCAAAATCGGTAACTTGGAGATGGTCAGCCTGCTGAGCACAGGACAAGTGGATGTCAACACCCA
GGACAGTGGTGGGTGGATGCCCATCATCTGGGCTGCAGAGCACAAGCACATCGAGGTGATCCGCATGCTATTGACGCAGG
GCGCTGATGTCATCCTCACTGACAACGAAGAAAACATCTGCCTGCACTGGGCCTCCTTCACCAGCAGCACCGCCATCGCT
GAAGTCCTTCTGAATGCATGCTGTGACCTCCACGCTGTCAACTACATATATATGATATATGGGGACACTCCCCTGCATAT
CGAAGCTCGGGAGAGCTACCATGACTGCATGCTGTTATTCCTGTCACATGGAGCCAACCCTGAGCTGTGAAACAAGGAGG
GGGACATGGCATGGGACCTGACTCCCGAGCACTCCAACGTGTGGTTTGTGCTTCAACTTAACCGCAAGCTCCGACTCAGG
GTAGGAAATCGGGCCATCTGCACAGAGAAGATCATCTCCCGGGATGTGGCTCGGGGCTATGAGAACGTGCCCATTCCCTG
TGTCAACAGTGTGGATGGGGAGCCCTGCCCCGAGGATTGCAAGTACGTCTTGGAAGACTGTGAGATGTCCACCATGAACA
TCGACCACAACATCACCCATCTGCAGCACTGCACGTGTGTGGACGACTGCTCCAGCTCCAACTGCCTGTGTGGCCGAGTC
AGCATCTAGTGCTAGTATGACAAGGATGGGCGATTGCTCCAGGAATTTAACAAGATTGAGCCCCCCACTGATTTTTTAGT
GTAACCAGGCATGCTTCTGCTGGAGAAACTTCAAGAACCGGGTCATACAGAGCGGCATCAAGGTTCGGCTACAGCTCTAC
CAAACAGCCAAGATGGGCTGGGGGGTCCATGCCCTGCAGACCATCCCACAGGGAACCTTCATCTGCAAGTGTCAGGGAGC
TGATGCTGAGGCTGATGTGAGAGAGGATGATTCTTACCTCTTCAACTAAGACAACAAGGATGGAGAGGTGTACTGCATTG
ATCCCCTTTACTATGGCAACATCAGCCAATTCATCAACCACCTGTGTGACCCCAACATCATTCCCATCTGGGTCTTCATG
CTGCACCAAGACCTGTGATTTCCATGCATTGCCTTCTTCAGTTCCCGAGACATCCGGACTGGGGAGGAGCTAAGGTTTGA
CTATGGCGACCGCTTCTGCGACATCAAAAGCAAATACTTCACCTGCCAGTGTGGCTCTGAGAAGTGCAAGCACTCAGCCA
AAGCCATTGCCCTAGAGCGGAGCCATCTGGCCCACCTGGACCCACACCCCGAGCTGCTGCCCGAGCTCAGCTCCCTGCCC
CTGTCAAC

Alignment

ORF - retro_cjac_3152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.52 %
• Parental protein coverage: 88.12 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SGNQSDRSGSSGRRKAKKKWRKDSPWVKPSRKRRKREPPRAKEPRGVNGVGSSGPSEYMEVPLGSLELPS
          SGNQSDRSGSSGR.KAKKKW.KDSPWVK.SRKRRK.EPPRAKEP.GVNGVGSSGP.EYMEVPLGSLELP.
Retrocopy SGNQSDRSGSSGRHKAKKKWLKDSPWVKSSRKRRKWEPPRAKEP*GVNGVGSSGPNEYMEVPLGSLELPR

Parental  EGTLSPNHAGVSNDTSSLETERGFEELPLCSCRMEAPKIDRISERAGHKCMATESVDGELSGCNAAILKR
          EGTLSPNH.GVSNDTS.LETERGFEELPLCSC.M.APK.D.ISERA.HK.MA.ESVDGELSGC.AAILKR
Retrocopy EGTLSPNHSGVSNDTSLLETERGFEELPLCSCCMKAPKTDHISERAEHKYMAMESVDGELSGCKAAILKR

Parental  ETMRPSSRVALMVLCETHRARMVKHHCCPGCGYFCTAGTFLECHPDFRVAHRFHKACVSQLNGMVFCPHC
          ET.RPSS.V.LMVLCETH.ARMVKH.CC.GCGYFC.A.TFL.CHPDF..AH.FHKACVSQLNGMVFCPHC
Retrocopy ETVRPSSHVTLMVLCETHHARMVKHQCCSGCGYFCMADTFLVCHPDFWMAHHFHKACVSQLNGMVFCPHC

Parental  GEDASEAQEVTIPRGDGVTPPAGTAAPAPPP-LSQDAPGRADTSQPSARMRGHGEPRRPPCDPLADTIDS
          GEDASEAQEVTIP.GDGVT.PAGTAAPAPPP..SQD.PGRA.TSQPSARMRGHGEP..PPC.PLADTIDS
Retrocopy GEDASEAQEVTIPHGDGVTTPAGTAAPAPPP<PSQDDPGRAGTSQPSARMRGHGEPWCPPCNPLADTIDS

Parental  SGPSLTLPNGGCLSAVGLPLGPGREALEKALVIQESERRKKLRFHPRQLYLSVKQGELQKVILMLLDNLD
          SGPSLTLPNGGCLS.VGLPLGPG.EALEKAL.IQESER.KKLRFH.RQLYL.VKQG.LQKVILMLLDNLD
Retrocopy SGPSLTLPNGGCLSTVGLPLGPGQEALEKALAIQESERQKKLRFHLRQLYLPVKQGKLQKVILMLLDNLD

Parental  PNFQSDQQSKRTPLHAAAQKGSVEICHVLLQAGANINAVDKQQRTPLMEAVVNNHLEVARYMVQRGGCVY
          PNF.SDQQSKR.PLHA.AQKGSVEICHVLLQAGA.INAVDKQQ..PLMEA.VNNHLEVARYMVQRG.C.Y
Retrocopy PNFESDQQSKRPPLHAGAQKGSVEICHVLLQAGAKINAVDKQQWVPLMEAMVNNHLEVARYMVQRGSCIY

Parental  SKEEDGSTCLHHAAKIGNLEMVSLLLSTGQVDVNAQDSGGWTPIIWAAEHKHIEVIRMLLTRGADVTLTD
          SKE.DGSTCLHHAAKIGNLEMVS.LLSTGQVDVN.QDSGGW.PIIWAAEHKHIEVIRMLLT.GADV.LTD
Retrocopy SKEVDGSTCLHHAAKIGNLEMVS-LLSTGQVDVNTQDSGGWMPIIWAAEHKHIEVIRMLLTQGADVILTD

Parental  NEENICLHWASFTGSAAIAEVLLNARCDLHAVNY----HGDTPLHIAARESYHDCVLLFLSRGANPELRN
          NEENICLHWASFT.S.AIAEVLLNA.CDLHAVNY.....GDTPLHI.ARESYHDC.LLFLS.GANPEL.N
Retrocopy NEENICLHWASFTSSTAIAEVLLNACCDLHAVNYIYMIYGDTPLHIEARESYHDCMLLFLSHGANPEL*N

Parental  KEGDTAWDLTPERSDVWFALQLNRKLRLGVGNRAIRTEKIICRDVARGYENVPIPCVNGVDGEPCPEDYK
          KEGD.AWDLTPE.S.VWF.LQLNRKLRL.VGNRAI.TEKII.RDVARGYENVPIPCVN.VDGEPCPED.K
Retrocopy KEGDMAWDLTPEHSNVWFVLQLNRKLRLRVGNRAICTEKIISRDVARGYENVPIPCVNSVDGEPCPEDCK

Parental  YISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIE-PPLIFECNQA
          Y..E.CE.STMNID.NITHLQHCTCVDDCSSSNCLCG..SI.C.YDKDGRLLQEFNKIE.PPLIF.CNQA
Retrocopy YVLEDCEMSTMNIDHNITHLQHCTCVDDCSSSNCLCGRVSI*C*YDKDGRLLQEFNKIE>PPLIF*CNQA

Parental  CSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLD
          C.CWRN.KNRV.QSGIKVRLQLY.TAKMGWGV.ALQTIPQGTFIC...G....DAEADVREDDSYLF..D
Retrocopy CFCWRNFKNRVIQSGIKVRLQLYQTAKMGWGVHALQTIPQGTFICKCQG---ADAEADVREDDSYLFN*D

Parental  NKDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWD
          NKDGEVYCID..YYGNIS.FINHLCDPNIIP..VFMLHQDL.FP.IAFFSSRDIRTGEEL.FDYGDRF.D
Retrocopy NKDGEVYCIDPLYYGNISQFINHLCDPNIIPIWVFMLHQDL*FPCIAFFSSRDIRTGEELRFDYGDRFCD

Parental  IKSKYFTCQCGSEKCKHSAEAIALEQSRLARLDPHPELLPELSSLP-PVN
          IKSKYFTCQCGSEKCKHSA.AIALE.S.LA.LDPHPELLPELSSLP.PVN
Retrocopy IKSKYFTCQCGSEKCKHSAKAIALERSHLAHLDPHPELLPELSSLP<PVN

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	0.13 RPM	12.74 RPM
SRP051959_heart	0.07 RPM	13.23 RPM
SRP051959_kidney	0.11 RPM	13.89 RPM
SRP051959_liver	0.19 RPM	5.16 RPM
SRP051959_lung	0.13 RPM	14.93 RPM
SRP051959_lymph_node	0.09 RPM	21.14 RPM
SRP051959_skeletal_muscle	0.11 RPM	4.65 RPM
SRP051959_spleen	0.25 RPM	17.37 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3152 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3152 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3152 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002489	1 retrocopy	retro_cjac_2209,
Callithrix jacchus	ENSCJAG00000037618	1 retrocopy	retro_cjac_3152 ,