RetrogeneDB ID: retro_cjac_4130

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:131601059..131601593(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRM2B
• Ensembl ID: ENSCJAG00000015923
• Aliases: None
• Description: ribonucleotide reductase M2 B (TP53 inducible) [Source:HGNC Symbol;Acc:17296]

Sequence

>retro_cjac_4130
GATATTTGGAAAATTATAAGAAAGCAAAGATTTCCTTCTGGATGGCCCAGGATGTGGACCTGTTCAAAGACATTCAGCAC
TGGGAAGCCCTGAAGCCTGAGGTAAGATATTTTATATCCCATATTCTGACTTTCTTTGTAGCATGTGATGGCATAGTTGA
TGAAAACTTGGTGGAGCAATTTGTCCAAGAAGTTCAGGCTACAGAAACCTGCTTCTATGGCTTCCAAATTGCTATGGAAA
ACATCTATTCTGACATGGATAATCTCTTTACTGACACATGTTAAAGACAACAAAGAAAGGGAATTTCTCTTCAATGCCAT
TGAAAGGATGCCTTGTGTCAAGAAGGAGGCAGATTGGGCCTTGTGTTGGATTGAGAACAAAGATGCTACCCACGGAGAAC
GTGTGGCAGCCTTTGCCATAGTAGAAGGCACCTTCTCTTATGGTTCTTTTGCATTGATATTCTGGCTCAAGAAACAATGA
ATGATGTCTGGCCTCACATTTTCTAATGACCTTATTAGCAGTGATGAGGGTTTA

Alignment

ORF - retro_cjac_4130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.48 %
• Parental protein coverage: 51.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DIWKM-YKQAQASFWTAEEVDLSKDLPHWNKLKADEKYFISHILAFFAASDGIVNENLVERFSQEVQVPE
          DIWK..YK.A..SFW.A..VDL.KD..HW..LK....YFISHIL.FF.A.DGIV.ENLVE.F.QEVQ..E
Retrocopy DIWKI<YKKAKISFWMAQDVDLFKDIQHWEALKPEVRYFISHILTFFVACDGIVDENLVEQFVQEVQATE

Parental  ARCFYGFQILIENVHSEMYSLLIDT-YIRDPKK-REFLFNAIETMPYVKKKADWALRWIADRKSTFGERV
          ..CFYGFQI..EN..S.M..L..DT......KK.REFLFNAIE.MP.VKK.ADWAL.WI.....T.GERV
Retrocopy T-CFYGFQIAMENIYSDMDNLFTDT<MLKTTKK<REFLFNAIERMPCVKKEADWALCWIENKDATHGERV

Parental  VAFAAVEGVFFSGSFAAIFWLKKRGLMPGLTFSNELISRDEGL
          .AFA.VEG.F..GSFA.IFWLKK...M.GLTFSN.LIS.DEGL
Retrocopy AAFAIVEGTFSYGSFALIFWLKKQ*MMSGLTFSNDLISSDEGL

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	6.97 RPM
SRP051959_heart	0.00 RPM	15.56 RPM
SRP051959_kidney	0.13 RPM	12.78 RPM
SRP051959_liver	0.00 RPM	10.51 RPM
SRP051959_lung	0.00 RPM	13.37 RPM
SRP051959_lymph_node	0.00 RPM	16.64 RPM
SRP051959_skeletal_muscle	0.00 RPM	18.39 RPM
SRP051959_spleen	0.00 RPM	15.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4130 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4130 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4130 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012265	4 retrocopies	retro_chof_1118, retro_chof_1233, retro_chof_277, retro_chof_692,
Callithrix jacchus	ENSCJAG00000006533	3 retrocopies	retro_cjac_2134, retro_cjac_2950, retro_cjac_3851,
Callithrix jacchus	ENSCJAG00000015923	1 retrocopy	retro_cjac_4130 ,
Echinops telfairi	ENSETEG00000020338	1 retrocopy	retro_etel_1219,
Gorilla gorilla	ENSGGOG00000003053	1 retrocopy	retro_ggor_3001,
Mus musculus	ENSMUSG00000022292	1 retrocopy	retro_mmus_988,
Otolemur garnettii	ENSOGAG00000004487	1 retrocopy	retro_ogar_2602,
Pan troglodytes	ENSPTRG00000020481	1 retrocopy	retro_ptro_3204,
Ictidomys tridecemlineatus	ENSSTOG00000008543	2 retrocopies	retro_itri_1555, retro_itri_877,
Tupaia belangeri	ENSTBEG00000008855	1 retrocopy	retro_tbel_3693,