RetrogeneDB ID: retro_cjac_2767

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:125095717..125096180(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEAF6
• Ensembl ID: ENSCJAG00000001927
• Aliases: None
• Description: None

Sequence

>retro_cjac_2767
CAACAGATCTATGCTTTTGAGGGAACTACATGGAAGACACTCAGATGTATGACAATATTACTCCTGGCTGGGATCGGTAT
CTGACCAACCAAATAAAAACTCCAATAGCAAAAATGATCGAAGGAATCGGAACTTTAAGGAAGCTGAGCAGCTCTTCAGT
AAATCCTTAGTTACCTCAGCAGCTGCTGAAGTGCGCTGGCAGGAGTTCAGGACTAGCTCACTGAAAAGAGGGAGCCAGGA
AGTAGGACAGAAAGTTAACACTGCTCCAGACTTCCAAGGTCAGGAAAACAAGCCGAGCAGGGAGTACCCTGAGGATATGG
ATGGATCTGTTCAGGGAGGGAAACTTCAGAAGTCTGCCTCATCTACTTCCTCAGGGAGTCACCACAGCAGCCATAAAATG
CGAAAGAATAAAAATCAGCACAGGATTGATCTGAAGTTAAACAAAAAACCACAAGCTGACTAT

Alignment

ORF - retro_cjac_2767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.96 %
• Parental protein coverage: 83.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KQIYAFEGS-YLEDTQMYGNIIRGWDRYLTNQ-KNSNSKNDRRNRK-FKEAERLFSKSSVTSAAAV-SAL
          .QIYAFEG..Y.EDTQMY.NI..GWDRYLTNQ..........R....FKEAE.LFSKS.VTSAAA..SAL
Retrocopy QQIYAFEGT<YMEDTQMYDNITPGWDRYLTNQ<NKNSNSKNDRRNRNFKEAEQLFSKSLVTSAAAE<SAL

Parental  AGVQDPLIEKREPGSGTES-DTSPDFHNQENEPSQEDPEDLDGSVQGVKPQKPASSTSSGSHHSSHKKRK
          AGVQD.L.EKREPGS.TES..T.PDF..QEN.PS.E.PED.DGSVQG.K.QK.ASSTSSGSHHSSHK.RK
Retrocopy AGVQD*LTEKREPGSRTES>NTAPDFQGQENKPSREYPEDMDGSVQGGKLQKSASSTSSGSHHSSHKMRK

Parental  NKNRHRIDLKLNKKPRADY
          NKN.HRIDLKLNKKP.ADY
Retrocopy NKNQHRIDLKLNKKPQADY

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	12.62 RPM
SRP051959_heart	0.02 RPM	19.73 RPM
SRP051959_kidney	0.00 RPM	17.04 RPM
SRP051959_liver	0.00 RPM	9.36 RPM
SRP051959_lung	0.00 RPM	22.30 RPM
SRP051959_lymph_node	0.00 RPM	24.73 RPM
SRP051959_skeletal_muscle	0.00 RPM	19.61 RPM
SRP051959_spleen	0.00 RPM	16.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2767 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2767 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2767 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001927	1 retrocopy	retro_cjac_2767 ,
Cavia porcellus	ENSCPOG00000025988	1 retrocopy	retro_cpor_1252,
Erinaceus europaeus	ENSEEUG00000013971	3 retrocopies	retro_eeur_362, retro_eeur_469, retro_eeur_654,
Macropus eugenii	ENSMEUG00000003403	3 retrocopies	retro_meug_1279, retro_meug_584, retro_meug_727,
Myotis lucifugus	ENSMLUG00000017128	2 retrocopies	retro_mluc_436, retro_mluc_960,
Otolemur garnettii	ENSOGAG00000006773	1 retrocopy	retro_ogar_2339,
Vicugna pacos	ENSVPAG00000001916	1 retrocopy	retro_vpac_566,