RetrogeneDB ID: retro_cjac_4047

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:20921502..20922532(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METT5D1
• Ensembl ID: ENSCJAG00000006142
• Aliases: None
• Description: None

Sequence

>retro_cjac_4047
AGATATTTTGAAACTGTGGCTAAATTACACATTCTCGTAATGCTGGATGAAGCTGTTCATTGTTTGTCACCACAAAATGA
CAGATTTTTCTAGATATGACATTTGGTTCGGGAAGGTACACAAAAACCACTCTACAGCAGTTAGACATTGTTCTGTATGC
CTTAGACAGGGACCCAACAGCTTATGCATTAGGTGAACATCTTTCAGAGTTGTATCCGAAACAAATCTGAGTTATGCTGG
GCCAATTCAGCCAGGCAGAAGCCTTATTAATGAAAGTTGGAGTGCAGCCAGGGACTTCAGATGGAGTTCTTATGGATCCT
GGGTGTTCCTCCATGCAACCTGATACTCACGAAAGAGTTTTTTCCCTTTGGAAAGATGGCCCCTTGGACATGAGGATGGA
TGGTGGCAGGTAACCTGATGTGCCCCTGCAGTTAATGTTGTGAATGCTTTAAATCAACAGGCACTTGCATCTACCCTAAG
AACATGTGGGAAGGAGAAGCATGCCAAGAAAATTGCTTCAGCAATTGTTCAGACATGCAGCATCTACCACATCACCAGAA
CCCAGCAGCTTGCCAGCATCGTCACAGGTGCATTTCCTCCCTCTGCTATTTATGCACAAAATGATGTGCTACAGCGATCG
ACGCATATTGCCACCAAGACTTTCCAGGCTCTTTGCATATTTTTGAACAATGAGCTCAATGAACTCTACACAGGACTAAA
GATGGCTTAGAAGTTTCTGAGACCTGGTGGTTGTCTTGTTGCCCTCTCTTTCCATTCACTAGAGGATCGCATTGTCAAAA
GGTTTTTGCCTGGAATAAGCATGACAGAAAGGTTTAACCTAAGTGTTAGACAGCAAATGATGAAAACATTGCAATTGGGT
TCAGATCATGAAAACATGGAAGAAGTCTCCATGAGAAGAGCTCCTTTAATGTGGGAATTGATATACAAGAAGGTGCTTAG
TCCACAAGATCAGGATGTACAAGATAACCCTAGAGGGTGCTCAGCCAAGCTTAGAGCAGCTATCAAATTA

Alignment

ORF - retro_cjac_4047 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.98 %
• Parental protein coverage: 84.73 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RNFETMVKLHIPVMVDEVVHCLSPQ-KGQIFLDMTFGSGGHTKAILQKESDIVLYALDRDPTAYALAEHL
          R.FET..KLHI.VM.DE.VHCLSPQ.K.QIFLDMTFGSG..TK..LQ...DIVLYALDRDPTAYAL.EHL
Retrocopy RYFETVAKLHILVMLDEAVHCLSPQ<K*QIFLDMTFGSGRYTKTTLQ-QLDIVLYALDRDPTAYALGEHL

Parental  SELYPKQIRAMLGRFSQAETLLMKAEVQPGTFDGVLMDLGCSSMQLDTSERGFSLRKDGPLDMRMDGDRY
          SELYPKQI..MLG.FSQAE.LLMK..VQPGT.DGVLMD.GCSSMQ.DT.ER.FSL.KDGPLDMRMDG.R.
Retrocopy SELYPKQI*VMLGQFSQAEALLMKVGVQPGTSDGVLMDPGCSSMQPDTHERVFSLWKDGPLDMRMDGGR*

Parental  PDMPT-AADVVNALDQQALASILRAYGEEKHAKKIASAIVQARSIYPITRTQQLASIIAGAFPPSAIYAR
          PD.P..A..VVNAL.QQALAS.LR..G.EKHAKKIASAIVQ..SIY.ITRTQQLASI..GAFPPSAIYA.
Retrocopy PDVPL<AVNVVNALNQQALASTLRTCGKEKHAKKIASAIVQTCSIYHITRTQQLASIVTGAFPPSAIYAQ

Parental  KDLLQRSTHIATKTFQALRIFVNNELNELHTGLKTAQKFLRPGGRLVALSFHSLEDRIVKRFLLGISMTE
          .D.LQRSTHIATKTFQAL.IF.NNELNEL.TGLK.A.KFLRPGG.LVALSFHSLEDRIVKRFL.GISMTE
Retrocopy NDVLQRSTHIATKTFQALCIFLNNELNELYTGLKMA*KFLRPGGCLVALSFHSLEDRIVKRFLPGISMTE

Parental  RFNLSVRQQVMKASRLDSDHENV-EVSMRRAPLMWELIHKKVLSPQSRDVQDNPRGRSAKLRAAIKL
          RFNLSVRQQ.MK...L.SDHEN..EVSMRRAPLMWELI.KKVLSPQ..DVQDNPRG.SAKLRAAIKL
Retrocopy RFNLSVRQQMMKTLQLGSDHENMEEVSMRRAPLMWELIYKKVLSPQDQDVQDNPRGCSAKLRAAIKL

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	4.15 RPM
SRP051959_heart	0.00 RPM	6.38 RPM
SRP051959_kidney	0.00 RPM	7.48 RPM
SRP051959_liver	0.00 RPM	11.03 RPM
SRP051959_lung	0.00 RPM	6.93 RPM
SRP051959_lymph_node	0.00 RPM	7.76 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.31 RPM
SRP051959_spleen	0.00 RPM	8.91 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4047 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4047 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4047 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006142	2 retrocopies	retro_cjac_3301, retro_cjac_4047 ,
Homo sapiens	ENSG00000169519	2 retrocopies	retro_hsap_1123, retro_hsap_4656,
Macaca mulatta	ENSMMUG00000013616	1 retrocopy	retro_mmul_870,
Nomascus leucogenys	ENSNLEG00000017865	2 retrocopies	retro_nleu_1093, retro_nleu_187,
Oryctolagus cuniculus	ENSOCUG00000014291	1 retrocopy	retro_ocun_536,
Pongo abelii	ENSPPYG00000003399	1 retrocopy	retro_pabe_3617,
Pan troglodytes	ENSPTRG00000003461	1 retrocopy	retro_ptro_680,