RetrogeneDB ID: retro_cjac_745

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:126146540..126147005(+)
• Located in intron of: ENSCJAG00000016853

Retrocopy information

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

Parental gene information

• Parental gene symbol: MGST1
• Ensembl ID: ENSCJAG00000021590
• Aliases: None
• Description: microsomal glutathione S-transferase 1 [Source:HGNC Symbol;Acc:7061]

Sequence

>retro_cjac_745
ATGGTTGACCTTTCCCAGCTAACGGACGATGAAGTGTTCAGGGCTTTTGCCTCCTATGCAACAATTATTCTTTCAAAAAT
GATGCTTATGAGCGCTGCGACTGCGTTCTATAGAATGACGAGAAAGGTTTTTGCCAACCCAGAAGACTCTGCAACATTTG
GCAAGGGAGAAAACGCCAAGAAGTATCTTCCAACAGATGACAGAGTAGAACGTGTACGCAGGGCTCACCTTAACGACCTT
GAAAACATTGTTCCGTTTCTGGGAATCGGGCTTCTGTATTCCCTGAGTGGTCCCGACCTCTCCACAGCCGTTCTGCACTT
CAGAATCTTTGTCGGAGGACGGATCTACCACACCATCGCGTACCTGACACCCCTTCCCCAGCCAAACAGAGCTTTGGGTT
TTTTTGTTGGATATGGGATTACTCTTTCCATGGCTTACAGGTTGCTGAAAAGTAGATTGTACCTG

Alignment

ORF - retro_cjac_745 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVDLSQLTDDEVFRAFASYATIILSKMMLMSAATAFYRMTRKVFANPEDCATFGKGENAKKYLRTDDRVE
          MVDLSQLTDDEVFRAFASYATIILSKMMLMSAATAFYRMTRKVFANPED.ATFGKGENAKKYL.TDDRVE
Retrocopy MVDLSQLTDDEVFRAFASYATIILSKMMLMSAATAFYRMTRKVFANPEDSATFGKGENAKKYLPTDDRVE

Parental  RVRRAHLNDLENIVPFLGIGLLYSLSGPDLSTAVLHFRIFVGARIYHTIAYLTPLPQPNRALGFFVGYGV
          RVRRAHLNDLENIVPFLGIGLLYSLSGPDLSTAVLHFRIFVG.RIYHTIAYLTPLPQPNRALGFFVGYG.
Retrocopy RVRRAHLNDLENIVPFLGIGLLYSLSGPDLSTAVLHFRIFVGGRIYHTIAYLTPLPQPNRALGFFVGYGI

Parental  TLSMAYRLLKSRLYL
          TLSMAYRLLKSRLYL
Retrocopy TLSMAYRLLKSRLYL

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	2.73 RPM	9.63 RPM
SRP051959_heart	0.86 RPM	2.39 RPM
SRP051959_kidney	0.80 RPM	1.53 RPM
SRP051959_liver	22.70 RPM	100.40 RPM
SRP051959_lung	1.06 RPM	2.54 RPM
SRP051959_lymph_node	0.71 RPM	0.39 RPM
SRP051959_skeletal_muscle	0.15 RPM	0.11 RPM
SRP051959_spleen	0.99 RPM	1.51 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_745 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_745 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_745 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013004	3 retrocopies	retro_chof_1564, retro_chof_1842, retro_chof_2298,
Callithrix jacchus	ENSCJAG00000021590	1 retrocopy	retro_cjac_745 ,
Echinops telfairi	ENSETEG00000007466	7 retrocopies	retro_etel_142, retro_etel_1541, retro_etel_1615, retro_etel_1727, retro_etel_2045, retro_etel_789, retro_etel_989,
Loxodonta africana	ENSLAFG00000002693	1 retrocopy	retro_lafr_976,
Myotis lucifugus	ENSMLUG00000002358	1 retrocopy	retro_mluc_1078,
Tupaia belangeri	ENSTBEG00000016248	6 retrocopies	retro_tbel_1229, retro_tbel_2494, retro_tbel_3452, retro_tbel_3654, retro_tbel_366, retro_tbel_4500,