RetrogeneDB ID: retro_cjac_3250

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:107888553..107888988(+)
• Located in intron of: ENSCJAG00000009419

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGOHB
• Ensembl ID: ENSCJAG00000021662
• Aliases: None
• Description: mago-nashi homolog B (Drosophila) [Source:HGNC Symbol;Acc:25504]

Sequence

>retro_cjac_3250
CTGACTATGGCTAGTGATTTCTCCCTGCGCTATTACATAGGGCACAAGGGCAGGCTTGGGCATGAGTTTCTGGAGTTCAA
ATTTCAGCCAGACACAAAGTTTAGATATGCCAGAAACAACGATTGCAAAAATGATGTCATGATCAAAAAAGAGGCTTATG
TACACGAGAGTGTAATGGAAGAACCGAAGGGAATTATTGACAGTGAAACTCCAAAGGTGATGCTTTGTGGCCTCCCCCAG
ACAGGGTTGGCCGACAGGAGCTTGAATTGTTATTGGAGATGAACACATATGTTTTACCACACCAAAAATAGGTTCTGTTG
TTGATGTAAATCAGGCAAAGGATCTGAAGGCCTTCGAGTATTTTACTATTTGGTTCAAGACTTGAAATGTTCAGTTTTCA
GTCTCCCTGGATGACACTTCAAGTTGAAACTGATT

Alignment

ORF - retro_cjac_3250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSMASDFYLRYYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIIDDSE
          ..MASDF.LRYY.GHKG..GHEFLEF.F.PD.K.RYA.N...KNDVMI.KEAYVH.SVMEE.K.II.DSE
Retrocopy LTMASDFSLRYYIGHKGRLGHEFLEFKFQPDTKFRYARNNDCKNDVMIKKEAYVHESVMEEPKGII-DSE

Parental  I-TKEDDALWPPPDRVGRQELE-IVIGDEHISFTTSKIGSLIDVNQSKD-PEGLRVFYYLVQDLKCLVFS
          ...K.D....PP.DRVGRQELE.IVIGDEHI.FTT.KIGS..DVNQ.KD..EGLRVFYYLVQDLKC.VFS
Retrocopy T<SKGDALWPPP-DRVGRQELE<IVIGDEHICFTTPKIGSVVDVNQAKD<SEGLRVFYYLVQDLKCSVFS

Parental  LIGLHFKIKPI
          L.G.HFK.K.I
Retrocopy LPG*HFKLKLI

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	2.84 RPM
SRP051959_heart	0.05 RPM	2.35 RPM
SRP051959_kidney	0.00 RPM	3.82 RPM
SRP051959_liver	0.00 RPM	3.81 RPM
SRP051959_lung	0.08 RPM	3.20 RPM
SRP051959_lymph_node	0.00 RPM	2.85 RPM
SRP051959_skeletal_muscle	0.28 RPM	2.23 RPM
SRP051959_spleen	0.00 RPM	3.07 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3250 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3250 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3250 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004382	1 retrocopy	retro_chof_1730,
Callithrix jacchus	ENSCJAG00000004538	1 retrocopy	retro_cjac_1902,
Callithrix jacchus	ENSCJAG00000021662	7 retrocopies	retro_cjac_1336, retro_cjac_1840, retro_cjac_1858, retro_cjac_2354, retro_cjac_3234, retro_cjac_3250 , retro_cjac_546,
Dasypus novemcinctus	ENSDNOG00000005997	4 retrocopies	retro_dnov_140, retro_dnov_347, retro_dnov_423, retro_dnov_891,
Echinops telfairi	ENSETEG00000016591	3 retrocopies	retro_etel_1022, retro_etel_1566, retro_etel_2147,
Homo sapiens	ENSG00000111196	1 retrocopy	retro_hsap_1360,
Macropus eugenii	ENSMEUG00000001782	1 retrocopy	retro_meug_324,
Macaca mulatta	ENSMMUG00000005082	1 retrocopy	retro_mmul_1246,
Monodelphis domestica	ENSMODG00000000462	1 retrocopy	retro_mdom_424,
Nomascus leucogenys	ENSNLEG00000003355	1 retrocopy	retro_nleu_1395,
Ochotona princeps	ENSOPRG00000000548	2 retrocopies	retro_opri_1171, retro_opri_308,
Pan troglodytes	ENSPTRG00000004679	2 retrocopies	retro_ptro_1179, retro_ptro_932,
Ictidomys tridecemlineatus	ENSSTOG00000000835	1 retrocopy	retro_itri_212,
Tupaia belangeri	ENSTBEG00000014820	7 retrocopies	retro_tbel_1250, retro_tbel_1393, retro_tbel_210, retro_tbel_2259, retro_tbel_2723, retro_tbel_2878, retro_tbel_451,
Tarsius syrichta	ENSTSYG00000010452	7 retrocopies	retro_tsyr_1730, retro_tsyr_1748, retro_tsyr_383, retro_tsyr_658, retro_tsyr_81, retro_tsyr_908, retro_tsyr_966,