RetrogeneDB ID: retro_cjac_3004

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:89348071..89348729(-)
• Located in intron of: ENSCJAG00000004976

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTM1
• Ensembl ID: ENSCJAG00000003123
• Aliases: None
• Description: glutathione S-transferase mu 1 [Source:HGNC Symbol;Acc:4632]

Sequence

>retro_cjac_3004
ATGCCCACGACAGTGGGGTACTGGGACCTCCGCAGGCTGGCCCACACCATCCGCCTGCTCCTGGAATACATAGACTCAAG
CTACAAGGAAAAGACCTATATGATGGGGGACGCTCCTGACTATGACAGAAGCCAGTGGCTGAAGGACAAATTCAAGCTAA
GCCTGGACTTTCCTAATCTGCCCTACTTGATTGATGGGGCTCACAAGATCACCTAGAGCAACGCCATCCTGCGCTACATT
GCCCGCAAGCACAACCTGTGTGGGGAGACAGAAGAGAAGAAGATTCGTGTGGACATTTTGGAGAACCAGACCACGGACAC
CCGGATGCAGCTGGTCATGATCTGCTACGACCCAGAACTTGAGAAACTGAAGGCAAAGAAAGTACTTGGAGGAACTCCCT
GAAAAGTTAAAGGTCTACTCACAGTTTCTGGGGAAGCGGCCATGGTTTGCAGGAGATAAGATCACCTTTGTGGATTTCCT
CGCCTATGACGTCCTTAACCACAACCGTATATTTGAGCCCTGCTGCCTGGATGCCTTCCCAATCCTGAAGGACTTCATCT
CCTGATTTGAGGGTTTGAAGAAGATCTCTACCTACATGAAGTCCAGCAGATTCGTCCCAGGTCCTTTGTTTGGAAAGTCA
GCTACATGGAACAGCAAA

Alignment

ORF - retro_cjac_3004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.18 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPMTLGYWDIRGLAHAIRLLLEYTDSSYEEKKYTMGDAPDYDRSQWLKEKFKLGLDFPNLPYLIDGAHKI
          MP.T.GYWD.R.LAH.IRLLLEY.DSSY.EK.Y.MGDAPDYDRSQWLK.KFKL.LDFPNLPYLIDGAHKI
Retrocopy MPTTVGYWDLRRLAHTIRLLLEYIDSSYKEKTYMMGDAPDYDRSQWLKDKFKLSLDFPNLPYLIDGAHKI

Parental  TQSNAILRYIARKHSLCGETEEEKIRVDILENQTMDTRMQLAMLCYNPEFEKLK-PKYLEELPEKLK-LY
          T.SNAILRYIARKH.LCGETEE.KIRVDILENQT.DTRMQL.M.CY.PE.EKLK..K.L...P.K.K..Y
Retrocopy T*SNAILRYIARKHNLCGETEEKKIRVDILENQTTDTRMQLVMICYDPELEKLKAKKVLGGTP*KVK>VY

Parental  SQFLGKRPWFAGDKITFVDFLAYDVLDQNRIFEPSCLDAFPNLKDFMSRFEGLKKISAYMKSSRFVPGLL
          SQFLGKRPWFAGDKITFVDFLAYDVL..NRIFEP.CLDAFP.LKDF.S.FEGLKKIS.YMKSSRFVPG.L
Retrocopy SQFLGKRPWFAGDKITFVDFLAYDVLNHNRIFEPCCLDAFPILKDFIS*FEGLKKISTYMKSSRFVPGPL

Parental  FGKSATWNSK
          FGKSATWNSK
Retrocopy FGKSATWNSK

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	0.38 RPM	24.03 RPM
SRP051959_heart	0.18 RPM	18.65 RPM
SRP051959_kidney	0.22 RPM	30.02 RPM
SRP051959_liver	0.28 RPM	15.47 RPM
SRP051959_lung	0.24 RPM	19.57 RPM
SRP051959_lymph_node	0.27 RPM	13.36 RPM
SRP051959_skeletal_muscle	0.11 RPM	8.84 RPM
SRP051959_spleen	0.23 RPM	22.65 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3004 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3004 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3004 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000879	1 retrocopy	retro_cjac_3321,
Callithrix jacchus	ENSCJAG00000003123	7 retrocopies	retro_cjac_1299, retro_cjac_2226, retro_cjac_2463, retro_cjac_2498, retro_cjac_3004 , retro_cjac_3084, retro_cjac_811,
Callithrix jacchus	ENSCJAG00000003168	1 retrocopy	retro_cjac_4,
Gorilla gorilla	ENSGGOG00000005148	2 retrocopies	retro_ggor_1913, retro_ggor_2459,
Nomascus leucogenys	ENSNLEG00000003194	2 retrocopies	retro_nleu_1546, retro_nleu_504,
Pongo abelii	ENSPPYG00000001064	2 retrocopies	retro_pabe_2218, retro_pabe_2990,
Pan troglodytes	ENSPTRG00000001061	2 retrocopies	retro_ptro_1859, retro_ptro_2468,