RetrogeneDB ID: retro_cjac_698

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:70325419..70326541(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ZNF277
• Ensembl ID: ENSCJAG00000016891
• Aliases: None
• Description: None

Sequence

>retro_cjac_698
ATGGTTGCTCCCAAGACCTAGGGAGCTGCAGCCCGACTGGAGGAAGACTGTGATAGGAGCTGCAGCACAGTTGGGGGTGT
AGGTTATGGGGGCAGTAAGGATTGTATCCTGGAGCCACTTTCCCTGCCAGAAAGTCCAGGTCGCACCACCACTTTAGAAG
GTTCTCCATCTGTGCCTTGTATTTTCTGTGAAGAACGTTTTCCTGTGGCTGAACAAGAGAAACTTCTGAAGCACATGAGT
ATTGAGCATAAGATTGCCATAGCTGATGTCAAATTGGTGGCTGATTTCCAAAGGTACCTTTATATTGGAGGAAGAGGTTC
ACTGAACAGCCCATCGCAGATTTTTGTAGTGTGATAAGAATTAATTCTGCTGCTCCATTTGAAGAACAAGATAATTATTT
TTTGTTATGTGATGTTTTACCAGAGGATAGAATTCTTCGAGAAGAGCTTCAGAAACAGAGACTGAAAGAAATTCTGGAAC
AACAGCAGCAAGAACAAAATGATACCAATTTTCATGGCATTTGTATATTTTGCAATGAAGAGTTCCTTGGAAACAGATCT
GTTCTTTTGGACCACATGGCAAGTGAATATGCTTCAACATTGGATTGCCAGACAACATCATAAACTGCAATGATTTTTGT
GTACATTACAGAAAAAGCTTGACAATTTGCAGTTCTTGTACTGTGAGAAGACCTTCAAGGAAAAAAATATGCTTAAAGAT
CACACGAGGAAACAATAGCCTCATAAGATTAATCCTAAGAACAGAGAATATGATCGATTTTATGTCATCAATTATTTGGA
ACTTGGAAAATCATGGGAAGAAGTTCAGTTGGAAGATGATCGGGAATTGCTGGACCATCATGAAGATGACTGGTCTGACT
GGGAAGAACACCCTGACTCTGCCATCTGCTTATTTGGTGAAAAGCAAGTTGAAACAATTGAGAAATTGTATGTCCACATG
GAGGATGCACATGAATTCGATCTCAAAATAGAGTCAGAAATTAGATTAAATTTCTATCAGCAAGTGAAACTGGTCAGTTT
TATTCGGAGGCAAGTTCACCAATGCAGATCTTTTGGCTGCCATGTGAAGTTCAAATCCAAAGCAGACTTAAGGACTCACA
TG

Alignment

ORF - retro_cjac_698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.28 %
• Parental protein coverage: 83.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAVPKTQGAVARLEEDRDGSCSTVGGVGYGDSKDCILEPLSLPESPGGTTTLEGSPSVPCIFCEEHFHVA
          M..PKT.GA.ARLEED.D.SCSTVGGVGYG.SKDCILEPLSLPESPG.TTTLEGSPSVPCIFCEE.F.VA
Retrocopy MVAPKT*GAAARLEEDCDRSCSTVGGVGYGGSKDCILEPLSLPESPGRTTTLEGSPSVPCIFCEERFPVA

Parental  EQDKLLKHMIIEHKIVIADVKLVADFQRYI-LYWRKRFTEQPITDFCSVIRINSTAPFEEQENYFLLCDV
          EQ.KLLKHM.IEHKI.IADVKLVADFQRY..LYWRKRFTEQPI.DFCSVIRINS.APFEEQ.NYFLLCDV
Retrocopy EQEKLLKHMSIEHKIAIADVKLVADFQRYL<LYWRKRFTEQPIADFCSVIRINSAAPFEEQDNYFLLCDV

Parental  LPEDRILREELQKQKLKEILEQQQQERNDNNFHGICMFCNEEFLGNRSVLLNHMAREHA-FNIGLPDNIV
          LPEDRILREELQKQ.LKEILEQQQQE.ND.NFHGIC.FCNEEFLGNRSVLL.HMA.E.A.FNIGLPDNI.
Retrocopy LPEDRILREELQKQRLKEILEQQQQEQNDTNFHGICIFCNEEFLGNRSVLLDHMASEYA<FNIGLPDNII

Parental  NCNEF-LCTLQKKLDNLQCLYCEKTFRDKNTLKDHMRKKQHRKINPKNREYDRFYVINYLELGKSWEEVQ
          NCN.F.LCTLQKKLDNLQ.LYCEKTF..KN.LKDH.RK....KINPKNREYDRFYVINYLELGKSWEEVQ
Retrocopy NCNDF<LCTLQKKLDNLQFLYCEKTFKEKNMLKDHTRKQ*PHKINPKNREYDRFYVINYLELGKSWEEVQ

Parental  LEDDRELLDNQEDDWSDWEEHPASAVCLFCEKQAETIEKLYVHMEDAHEFNLLKIKSELGLNFYQQVKLV
          LEDDRELLD..EDDWSDWEEHP.SA.CLF.EKQ.ETIEKLYVHMEDAHEF..LKI.SE..LNFYQQVKLV
Retrocopy LEDDRELLDHHEDDWSDWEEHPDSAICLFGEKQVETIEKLYVHMEDAHEFD-LKIESEIRLNFYQQVKLV

Parental  NFIRRQVHQCRCYGCHVKFKSKADLRTHM
          .FIRRQVHQCR..GCHVKFKSKADLRTHM
Retrocopy SFIRRQVHQCRSFGCHVKFKSKADLRTHM

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	6.79 RPM
SRP051959_heart	0.05 RPM	9.79 RPM
SRP051959_kidney	0.00 RPM	15.18 RPM
SRP051959_liver	0.06 RPM	15.05 RPM
SRP051959_lung	0.02 RPM	13.83 RPM
SRP051959_lymph_node	0.02 RPM	7.49 RPM
SRP051959_skeletal_muscle	0.00 RPM	9.06 RPM
SRP051959_spleen	0.04 RPM	12.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_698 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_698 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_698 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016891	2 retrocopies	retro_cjac_558, retro_cjac_698 ,
Mus musculus	ENSMUSG00000055917	1 retrocopy	retro_mmus_3684,
Otolemur garnettii	ENSOGAG00000005326	1 retrocopy	retro_ogar_1774,