RetrogeneDB ID: retro_cjac_1895

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:29874787..29875533(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMT
• Ensembl ID: ENSCJAG00000003962
• Aliases: None
• Description: Aminomethyltransferase [Source:UniProtKB/TrEMBL;Acc:F6PIE6]

Sequence

>retro_cjac_1895
CTCATGCAGGACAAGGTCAGGGAGCTTCAGAACCAGGGCAGAGATGTGGGCCTGGAGGTGCTGGATAATGCCTGCTAGCC
CTGCGAGGCCCCATTGCAGCCCAGGTGCTACAGGGTGGCGTGGCAGATGACCTGAGGAAACTGTCCTTCATGACCAGTGC
TGTGATGGAGGTGTTTGGTGTGTCTGGTTGCCGCGTGACCTGCTGTGGCTACACAAGAGATGACAGTGTGGAGATCTCGG
TGCTGGCAGTGGGAGCAGTTCACCTGGCAACAGCTCTTCTGGAAAACCCAGAGGTGAAGTTGGCAGGGTTGGCCGCGAGG
GATAGCCTGCGCCTGGAGGCAGGCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACACCTGTGGAGGGCAGCCT
CAGTTGGACACTGGGGAAGTGCCGTCAATCTGCTATGGACTTCCCTGGAGCCAAGGTCACTGTTCCCCAGCTGAAGGGCA
AGGTTTAGCGGAAGCGTGTGGGCTTGATGTGTGAGGGGGCCCTGAGGCGGGCGCACAGTCCCATCCTGAACATGGAGGGT
ACCATGACTGGTACTGTGACTAGTGGCTGCCCCTCACCCTCTCTGAAGAAGAATGTGGTGATGGGTTATGTGCCCTGCAA
GTACAATCGTCCAGAAACAAAGCTGCTGGTAGAGGTGCAGCAGAAGCAGCAGATGGCTGTGGTCAGCAAGATGCTCTTTG
TGCCCACGAACTACTATACCTTCAAA

Alignment

ORF - retro_cjac_1895 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.6 %
• Parental protein coverage: 61.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LMQDKVRELQNQGRDVGLEVLDNA-LLALQGPTAAQVLQAGVADDLRKLPFMTSAVMEVFGVSGCRVTRC
          LMQDKVRELQNQGRDVGLEVLDNA.LLAL.GP.AAQVLQ.GVADDLRKL.FMTSAVMEVFGVSGCRVT.C
Retrocopy LMQDKVRELQNQGRDVGLEVLDNA<LLALRGPIAAQVLQGGVADDLRKLSFMTSAVMEVFGVSGCRVTCC

Parental  GYTGEDGVEISVPAAGAVHLATALLQDPEVKLAGLAARDSLRLEAGLCLYGNDIDEHTTPVEGSLSWTLG
          GYT..D.VEISV.A.GAVHLATALL..PEVKLAGLAARDSLRLEAGLCLYGNDIDEHTTPVEGSLSWTLG
Retrocopy GYTRDDSVEISVLAVGAVHLATALLENPEVKLAGLAARDSLRLEAGLCLYGNDIDEHTTPVEGSLSWTLG

Parental  KRRRAAMDFPGAKVIVPQLKGKVQRRRVGLMCEGAPMRAHSPILNMEGTMIGTVTSGCPSPSLKKNVAMG
          K.R..AMDFPGAKV.VPQLKGKV.R.RVGLMCEGA..RAHSPILNMEGTM.GTVTSGCPSPSLKKNV.MG
Retrocopy KCRQSAMDFPGAKVTVPQLKGKV*RKRVGLMCEGALRRAHSPILNMEGTMTGTVTSGCPSPSLKKNVVMG

Parental  YVPCEYSRPGTKLMVEVRRKQQMAVVSKMPFVPTNYYTLK
          YVPC.Y.RP.TKL.VEV..KQQMAVVSKM.FVPTNYYT.K
Retrocopy YVPCKYNRPETKLLVEVQQKQQMAVVSKMLFVPTNYYTFK

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	0.00 RPM	2.51 RPM
SRP051959_heart	0.00 RPM	9.75 RPM
SRP051959_kidney	0.00 RPM	13.62 RPM
SRP051959_liver	0.00 RPM	7.97 RPM
SRP051959_lung	0.02 RPM	9.78 RPM
SRP051959_lymph_node	0.00 RPM	8.33 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.99 RPM
SRP051959_spleen	0.00 RPM	9.73 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1895 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1895 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1895 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011489	1 retrocopy	retro_cfam_1035,
Callithrix jacchus	ENSCJAG00000003962	1 retrocopy	retro_cjac_1895 ,
Homo sapiens	ENSG00000145020	1 retrocopy	retro_hsap_2953,
Monodelphis domestica	ENSMODG00000012973	1 retrocopy	retro_mdom_1809,
Pongo abelii	ENSPPYG00000013871	1 retrocopy	retro_pabe_2449,
Rattus norvegicus	ENSRNOG00000050214	1 retrocopy	retro_rnor_1397,