RetrogeneDB ID: retro_cjac_1749

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:28833368..28834088(-)
• Located in intron of: ENSCJAG00000018527

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAT2B
• Ensembl ID: ENSCJAG00000015401
• Aliases: None
• Description: None

Sequence

>retro_cjac_1749
ATGGTGGGGCGGGAGAAAGAGACCTCTATACACTTTGTTCCCGGGAGCTGCTGGCTGGTGGAGGAGGAAGTTAACATCCC
CAATAGGAGGGTTCTGGTTACTGGTGCCACTGGGCTTCTTGGCAGAGCTGTACACAGAGAATTTCAGCAGAATAATTGGC
ATGCTGTTGGCTGTGGTTTTAGAAGAGCAAGACCAAAATTTGAACAGGTTAATCTATTGGATTCTAATGCAGTTCATCAC
ATCATTCATGATTTTCAGCCCCATGTTATAGTACACTGTGCAGCAGAGAGAAGACCGGATGTTGTAGAAAATCAGCCAGA
TGCTGCCTCTCAACTTAATGTGGATGCTTCTGGGAATGTAGCAAAGGAAGCAGCTGCTGTTGGAGCATTTCTCATCTACA
TTAGCTCAGATTACGTATTTGATGGAACAAATCCACCTTACAGAGAGGAAGACATACCAGCTCCACTAAATTTGTATGGC
AAAACAAAATTAGATGGAGAAAAGGCTGTCCTGGAGAACAATCTAGGAGCTGCTGTTTTGAGGATTCCTATTCTATATGG
GGAGGTTGAAAAGCTCGAAGAAAGTGCTGTGACTGTTACGTTTGACAAAGTGCAGTTCAGCAACAAGTCAGCAAACGTGG
ATCACTGGCAGCAGAGGTTCCCCACACACGTCAAAGATGTGGCCACTGTGTGCCGGCAGCTAGCAGAGAAGAGAATGCTG

Alignment

ORF - retro_cjac_1749 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.5 %
• Parental protein coverage: 71.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVGREKELSIHFVPGSCRLVEEEVNIPNRRVLVTGATGLLGRAVHKEFQQNNWHAVGCGFRRARPKFEQV
          MVGREKE.SIHFVPGSC.LVEEEVNIPNRRVLVTGATGLLGRAVH.EFQQNNWHAVGCGFRRARPKFEQV
Retrocopy MVGREKETSIHFVPGSCWLVEEEVNIPNRRVLVTGATGLLGRAVHREFQQNNWHAVGCGFRRARPKFEQV

Parental  NLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNLAKEAAAVGAFLIYISSDYVF
          NLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGN.AKEAAAVGAFLIYISSDYVF
Retrocopy NLLDSNAVHHIIHDFQPHVIVHCAAERRPDVVENQPDAASQLNVDASGNVAKEAAAVGAFLIYISSDYVF

Parental  DGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVMFDKVQFSNKS
          DGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTV.FDKVQFSNKS
Retrocopy DGTNPPYREEDIPAPLNLYGKTKLDGEKAVLENNLGAAVLRIPILYGEVEKLEESAVTVTFDKVQFSNKS

Parental  ANMDHWQQRFPTHVKDVATVCRQLAEKRML
          AN.DHWQQRFPTHVKDVATVCRQLAEKRML
Retrocopy ANVDHWQQRFPTHVKDVATVCRQLAEKRML

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	0.02 RPM	12.42 RPM
SRP051959_heart	0.02 RPM	26.42 RPM
SRP051959_kidney	0.07 RPM	30.62 RPM
SRP051959_liver	0.02 RPM	15.01 RPM
SRP051959_lung	0.05 RPM	26.40 RPM
SRP051959_lymph_node	0.07 RPM	32.69 RPM
SRP051959_skeletal_muscle	0.13 RPM	20.05 RPM
SRP051959_spleen	0.00 RPM	36.09 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1749 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1749 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1749 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012350	1 retrocopy	retro_btau_387,
Callithrix jacchus	ENSCJAG00000015401	1 retrocopy	retro_cjac_1749 ,
Macaca mulatta	ENSMMUG00000013980	1 retrocopy	retro_mmul_2019,
Ictidomys tridecemlineatus	ENSSTOG00000009459	1 retrocopy	retro_itri_1696,
Tursiops truncatus	ENSTTRG00000001154	1 retrocopy	retro_ttru_1573,