RetrogeneDB ID: retro_cjac_1366

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:94585004..94585985(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NMT1
• Ensembl ID: ENSCJAG00000012649
• Aliases: None
• Description: None

Sequence

>retro_cjac_1366
AAAGAACTGTACACCCTCCTGAATGAGAACTATGTGGAAGATGATGACAACATGTTCTGATTTGATTATTCCCCAGAGTT
TCTTTTGTGGGCTCTCTGGCCACCCGGCTAGCTCCCCCAGTGGCACTGTGGGGTTTGAGTGGTCTCAAGCCGGAAATTGG
TTGGGTTCATTAGTGCCATACCAGCAAACATCCATATCTATGACACAGAGAAGAAGATGGTGGAGATCAACTTCCTGTGT
GTCCATAAGAAGCTGCGTTCCAAGAGGGTGGCTCCAGTCCTGATCCAAGAGATCTCCAGGCGGGTTCATCTGGAGGGCAT
CTTCCAGGCTGTTTACACTGCCGGGGTGGTACTACCAAAGCCTGTTGGCACCTGCAGGTATTGGCATCAGTCCCTAAACC
TACAGAAGCTGGTTGAAGTGAAGTTCTCCCACCTGAACAGAAATATGACCATGCAGCGCACCATGAAGCTGTACCGACTG
CCAGAGACTCCCAAGACAACTGGGCTTTGACCAATGGGAAAAAAGGACATTCCAGTAGTGCACCAGCTCCTCACCAGGTA
CTTGAAGCAGTTTCACCTCATGCCAGTCATGAGCCAGGAGGAGGTGGAGCACTGGTTCTATCCCCAGGAGAACATCATTG
ACACTTTTGTGGTGGAGAATACAAATGGAGAGGTGATGGATTTCCTGAGCTTTTCTACGCTGCCCTCCACCATCATGAAC
CATCCAACCCACAAGAGTCTCAAAGCTACTTATTCTTTCTACAATGTTCACACCCAGACCCCCCTTCTAGACCTCATGAG
CGATGCCCTTATTCTCACCAAAATGAAAGAGTTCAATGTGTTCAATGCACTGGATCTCATGGAGAACAAAACCTTCTTGG
AGAAGCTCAAGTTTGGCATAGGGGACGGCAACCTGCAGTATTACCTTTAATACTGGAAATGCCCCAGCATGGGGGCAGAG
AAGGTTGGGCTGGTGCTACAA

Alignment

ORF - retro_cjac_1366 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.35 %
• Parental protein coverage: 65.66 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTE
          KELYTLLNENYVEDDDNMF.FDYSPEFLLWAL.PPG.LPQWHCGV.VVSSRKLVGFISAIPANIHIYDTE
Retrocopy KELYTLLNENYVEDDDNMF*FDYSPEFLLWALWPPG*LPQWHCGV*VVSSRKLVGFISAIPANIHIYDTE

Parental  KKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEV
          KKMVEINFLCVHKKLRSKRVAPVLI.EI.RRVHLEGIFQAVYTAGVVLPKPVGTCRYWH.SLN..KL.EV
Retrocopy KKMVEINFLCVHKKLRSKRVAPVLIQEISRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHQSLNLQKLVEV

Parental  KFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMEKKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQE
          KFSHL.RNMTMQRTMKLYRLPETPKT.GL.PM.KKDIPVVHQLLTRYLKQFHL.PVMSQEEVEHWFYPQE
Retrocopy KFSHLNRNMTMQRTMKLYRLPETPKTTGL*PMGKKDIPVVHQLLTRYLKQFHLMPVMSQEEVEHWFYPQE

Parental  NIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDV
          NIIDTFVVEN.NGEV.DFLSF.TLPSTIMNHPTHKSLKA.YSFYNVHTQTPLLDLMSDAL.L.KMK.F.V
Retrocopy NIIDTFVVENTNGEVMDFLSFSTLPSTIMNHPTHKSLKATYSFYNVHTQTPLLDLMSDALILTKMKEFNV

Parental  FNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ
          FNALDLMENKTFLEKLKFGIGDGNLQYYL..WKCPSMGAEKVGLVLQ
Retrocopy FNALDLMENKTFLEKLKFGIGDGNLQYYL*YWKCPSMGAEKVGLVLQ

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	0.29 RPM	16.51 RPM
SRP051959_heart	0.05 RPM	24.96 RPM
SRP051959_kidney	0.67 RPM	20.77 RPM
SRP051959_liver	0.82 RPM	29.65 RPM
SRP051959_lung	0.02 RPM	21.39 RPM
SRP051959_lymph_node	0.05 RPM	24.38 RPM
SRP051959_skeletal_muscle	0.07 RPM	39.94 RPM
SRP051959_spleen	0.99 RPM	23.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1366 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1366 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1366 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012649	1 retrocopy	retro_cjac_1366 ,
Microcebus murinus	ENSMICG00000016650	2 retrocopies	retro_mmur_1526, retro_mmur_715,
Otolemur garnettii	ENSOGAG00000012938	1 retrocopy	retro_ogar_1822,
Tursiops truncatus	ENSTTRG00000006270	1 retrocopy	retro_ttru_561,