RetrogeneDB ID: retro_cjac_1676

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:21477041..21478106(-)
• Located in intron of: ENSCJAG00000005369

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRMT2B
• Ensembl ID: ENSCJAG00000004570
• Aliases: None
• Description: None

Sequence

>retro_cjac_1676
GCTCAAGGTGAAATTTTACAAAGACTGGAATCTCACATCCAAATGCTCAATGGAGTCACTGTGACAAGAGCTGCACCCAA
ATCTGAGGGGCTGTCTTGTCTCCTCCATCCTCTTATACCATCTCCTGTCATTGGTACTACAGATATAAGTCCACCTTCTC
TGTGAATCCAGGTCCAGATGGCAATCCAAAGACTGTGGAGTGTGACCGGGGAACTTGGAGAGATGGGAACATCATCTGTG
TATAGTCTAGCCATTTGAAAGACGTCCTTGAGAAACACACTCACGTGACACAGTACTATGAAGTATTCCTTCCACAGTCT
CCAATAGAGCCCTGCCTTCTACTTCATGAAGGTGGATATTGGTGTAAGCTCACAGTCCACACCAGTAGCCTAAGGCACAC
AATGGCTGTCATCACATTCCATCCTTCGGAATTAAGTCAGGAGGAGCTCCATGTTCAGAAGGAGACTATAAAGGAATGTT
TCATTAAAAGTCTTGGAGCAGTGTGTGGCTTGACCTCACCTGACTTCCAGGAAAGCACCATGACCCTGTTTTAGCCACCA
TCAGTCCACCTACCAGCTGTTGTTTAGGGAACCTCACATCTTTCAAGAGCTCCTGGGCTTGAAGATCTGCCTGTCTCCAG
ATGCCTTTTTCCAGATTAACACTGCTGGTGCTGAGATGCTGTAATCAATTTTGGGGAAGCCAATGGAAGTGAACTCTAAC
ACTCTCCTCCTTGCCATCTACTGTGGAACTGGTGTGATCAGCCTCTCTCTGGCCCAGCTACATCACAGGTCCTTGGGATT
TCGCTGGTGGAGCAGGCAGTGGAGGATGCCAGGTGGACTGCAGCCTGCAGTGGCATCACCAGCTTTGAGTTTCACACTGG
TTAAGCAGAGAAGATGTTTTCCAGGGCTGCTAAAGTCAAAGGAAGATAGACGGTTACTTGTGGCTGTGGTGAACCCAGCC
CATGCTGAACTGCATTACAAGAAGGTTCAAGTCATTTGAAACTTCAGGGCCCTCTGCATACTAGCTTTTGATCGCTTCAA
GCCCCATGATGAAACCACAAGGAAT

Alignment

ORF - retro_cjac_1676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.36 %
• Parental protein coverage: 70.44 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AQKKILQRLESYIQMLNGVDVTTAVPKSERLSCLLHPIIPSPVING-YRNKSTFSVNRGPDGNPKTVGYY
          AQ..ILQRLES.IQMLNGV.VT.A.PKSE.LSCLLHP.IPSPVI...YR.KSTFSVN.GPDGNPKTV...
Retrocopy AQGEILQRLESHIQMLNGVTVTRAAPKSEGLSCLLHPLIPSPVIGT<YRYKSTFSVNPGPDGNPKTVECD

Parental  LGTWRGGNIVCVQSNHLKNIPEKHSQVAQYYEIFLRQSPMEPCLVFHEGGYWRELIVRTNSQGHTMAIIT
          .GTWR.GNI.CV.S.HLK...EKH..V.QYYE.FL.QSP.EPCL..HEGGYW..L.V.T.S..HTMA.IT
Retrocopy RGTWRDGNIICV*SSHLKDVLEKHTHVTQYYEVFLPQSPIEPCLLLHEGGYWCKLTVHTSSLRHTMAVIT

Parental  LHPQKLSQEELRGQKEIVKEFFIKGPGAACDLTSLYFQESTMTR-CSHQQSPFELLFGEPYIFEELLSLK
          .HP..LSQEEL..QKE..KE.FIK..GA.C.LTS..FQESTMT...SH.QS...LLF.EP.IF.ELL.LK
Retrocopy FHPSELSQEELHVQKETIKECFIKSLGAVCGLTSPDFQESTMTL>FSHHQSTYQLLFREPHIFQELLGLK

Parental  IRISPDAFFQINTAGAEMLYRTVGELAGVNSDTILLDICCGTGVIGLSLAQ-HTSQVLGIELVEQAVEDA
          I..SPDAFFQINTAGAEML....G....VNS.T.LL.I.CGTGVI.LSLAQ..TSQVLGI.LVEQAVEDA
Retrocopy ICLSPDAFFQINTAGAEML*SILGKPMEVNSNTLLLAIYCGTGVISLSLAQ<ATSQVLGISLVEQAVEDA

Parental  RWTAAYNGITNSEFHTGRAEKI-LPGLLKSKEDGQSIVAVVNPARAGLHYKVVQAIRNCRAIRRLVFVSC
          RWTAA..GIT..EFHTG.AEK...PGLLKSKED....VAVVNPA.A.LHYK.VQ.I.N.RA...L.F...
Retrocopy RWTAACSGITSFEFHTG*AEKM>FPGLLKSKEDRRLLVAVVNPAHAELHYKKVQVI*NFRALCILAFDRF

Parental  KLHGETTRN
          K.H.ETTRN
Retrocopy KPHDETTRN

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	0.38 RPM	6.55 RPM
SRP051959_heart	1.93 RPM	7.47 RPM
SRP051959_kidney	0.38 RPM	11.20 RPM
SRP051959_liver	0.41 RPM	10.05 RPM
SRP051959_lung	0.98 RPM	8.44 RPM
SRP051959_lymph_node	0.82 RPM	10.68 RPM
SRP051959_skeletal_muscle	2.58 RPM	3.49 RPM
SRP051959_spleen	0.44 RPM	9.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1676 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1676 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004570	1 retrocopy	retro_cjac_1676 ,
Homo sapiens	ENSG00000188917	1 retrocopy	retro_hsap_272,
Gorilla gorilla	ENSGGOG00000023759	1 retrocopy	retro_ggor_319,
Macropus eugenii	ENSMEUG00000006532	2 retrocopies	retro_meug_1325, retro_meug_74,
Macaca mulatta	ENSMMUG00000010394	1 retrocopy	retro_mmul_567,
Monodelphis domestica	ENSMODG00000025630	1 retrocopy	retro_mdom_77,
Nomascus leucogenys	ENSNLEG00000007522	1 retrocopy	retro_nleu_1485,
Pongo abelii	ENSPPYG00000020545	1 retrocopy	retro_pabe_397,
Pan troglodytes	ENSPTRG00000023413	1 retrocopy	retro_ptro_228,