RetrogeneDB ID: retro_cjac_922

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:69892749..69893323(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: INO80C
• Ensembl ID: ENSCJAG00000021025
• Aliases: None
• Description: None

Sequence

>retro_cjac_922
GCGGCTCAAATTCCAATTGTGGCCACCGCTTCCGCTACTCGAATAGTCCGGAACAGCAAGAAGAGACCGGCCAGCCCTGC
CCACAGCAGCAACAGTAGCGGCGGGGACTATGGTGCCCGTAAAGAGGAAAAAGTGTCCGCCTCCAGCTTTGTGCAGGGTA
TCAGCATAGAAGCCACGAGTCGGAATAAAATGGTGCCCTCTGAGTTTAGCAGAGGACCTGTGGAAAAAGCTGCCAAACCT
TTGCCATCTAAGGATCCCAACTTGTGCACTCTGGCCACGGTGGCGCAGTAGCTGGCAGGAAGAACAGAACCTGGAAGAAC
CTGAAACAAATCCTCGCTTCAGAAAGGGCGTTGTGGGGCAACTGAACAGTCCTCACTACTTCAGTATTGATGCACCTCCA
TCCTTTAAGCCAGCTAAGAAGTATTCCGATGTTTCAGGTCTTCTTCCCAACTACACAGACCCCCAGAGCAAACCGCGGTT
CAGCACCATGGAAGACTTGTCCCACATTCGGAGGCTACCCTCCGACGTTGTCACCAGCTACCTGGACCTGAGGAAAGCCA
CTAGTGTCGTTCCC

Alignment

ORF - retro_cjac_922 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.9 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAQITIVATTYTPRIVRDSKKRPASPSHNS-SSGGGYGSSKKKKVCASSFAQGISMEAMSENKMVPSEFS
          AAQI.IVAT....RIVR.SKKRPASP.H.S.SSGG.YG..K..KV.ASSF.QGIS.EA.S.NKMVPSEFS
Retrocopy AAQIPIVATASATRIVRNSKKRPASPAHSSNSSGGDYGARKEEKVSASSFVQGISIEATSRNKMVPSEFS

Parental  TGPVEKATKPLPFKDPNF-VHSGHGGAVAGKKNRTWKNLKQILASERAL-PWQLNDPNYFSIDAPPSFKP
          .GPVEKA.KPLP.KDPN..VHSGHGGAVAG.KNRTWKNLKQILASERAL...QLN.P.YFSIDAPPSFKP
Retrocopy RGPVEKAAKPLPSKDPNL<VHSGHGGAVAGRKNRTWKNLKQILASERAL<VGQLNSPHYFSIDAPPSFKP

Parental  AKKYSDVSGLLANYTDPQSKLRFSTIEEFSYIRRLPSDVVTGYLALRKATSIVP
          AKKYSDVSGLL.NYTDPQSK.RFST.E..S.IRRLPSDVVT.YL.LRKATS.VP
Retrocopy AKKYSDVSGLLPNYTDPQSKPRFSTMEDLSHIRRLPSDVVTSYLDLRKATSVVP

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	4.26 RPM
SRP051959_heart	0.00 RPM	3.82 RPM
SRP051959_kidney	0.00 RPM	3.51 RPM
SRP051959_liver	0.02 RPM	3.14 RPM
SRP051959_lung	0.05 RPM	4.00 RPM
SRP051959_lymph_node	0.05 RPM	4.89 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.54 RPM
SRP051959_spleen	0.08 RPM	4.14 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_922 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_922 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_922 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021025	1 retrocopy	retro_cjac_922 ,
Myotis lucifugus	ENSMLUG00000030708	3 retrocopies	retro_mluc_118, retro_mluc_1892, retro_mluc_1942,
Mus musculus	ENSMUSG00000047989	2 retrocopies	retro_mmus_1358, retro_mmus_1410,