RetrogeneDB ID: retro_cjac_1762

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:14248238..14249090(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARRDC2
• Ensembl ID: ENSCJAG00000036002
• Aliases: None
• Description: arrestin domain containing 2 [Source:HGNC Symbol;Acc:25225]

Sequence

>retro_cjac_1762
CGCGGCGGAGCGGTCACCCACTGGCTGGAGGGTCGCAACGTGGGCGTCAACGCCGTGTCCAGCTACTACGCGGCAGCCGA
GACCTACTTGCGGCGGCGGCAGCTGCTGCTTCGAGACACGGGGGAGACCACGACGCTGCCTCCTGGGTGCCATGAGTTCC
TGTTCAACTTCCAGCTGCCCCCGACCCTGGTGACATCCTTCGAGGGCAAACACGGTAGTGTCCGTTACTGTATCAAGGCT
ACCCTGCACCGGCCCTGGATCCCAGCACGCAGGGCAAGGAAGGTGTTCACTGTCATCGAGCCTGTCGACATCAACACGCC
CGTCCTGCTGGCACCTCAAGCGGGGGCTCAGGAAAAGGTCGACCGATCCTGGTACCATAACCGTGGCCTCGTCTCCCTTT
CGGCCAAGATCGACCGCAAGAGCTACACACCAGGAGAGGTCATCCCCGTCTTTGCCAAGATGGACAACAGCTCCACGAGT
CCTGTGCTGCCTCGGGCGACCGTGGTGCAGACGCAGATGTTCATGGCCCGAGGCGCCTGAAAGCAGAAACAGGCAGTGGT
GGCCACACTCGCGGGCGAGCCGGTGGGCCCGGGACAGCGGGCGGTGTGGCAGGGCCGGGCGCTGCGGATACCCCCGGTGG
GTCCTTCTATCCTGCACTGCCGCGTTCTCCACGTGGACTACGCACTCAAGGTCTGCGTGGACATCCTGGGCACATCCAAG
CTACTGCTGGAGCTGCCACTGGTGATCGGCACTATCCCCTTGCACACCTTCGGCAGCCGTTCCTCCAGTGTGGGCAGCCA
CGCCAGCTTCCTGCTGGACTTGGGGCTGGGGGCCTTGCCGGAGCGGCCCGAG

Alignment

ORF - retro_cjac_1762 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.9 %
• Parental protein coverage: 70.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGGAVTHWLEGRSVGVNAVSSDYAAAETYLRRRQLLLRDTGETTTLPPGRHEFLFSFQLPPTLVTSFEGK
          RGGAVTHWLEGR.VGVNAVSS.YAAAETYLRRRQLLLRDTGETTTLPPG.HEFLF.FQLPPTLVTSFEGK
Retrocopy RGGAVTHWLEGRNVGVNAVSSYYAAAETYLRRRQLLLRDTGETTTLPPGCHEFLFNFQLPPTLVTSFEGK

Parental  HGSVRYCIKATLHRPWIPARRARKVFTVIEPVDINTPALLAPQAGAQEKVARSWYRNRGLISLSAKIDRK
          HGSVRYCIKATLHRPWIPARRARKVFTVIEPVDINTP.LLAPQAGAQEKV.RSWY.NRGL.SLSAKIDRK
Retrocopy HGSVRYCIKATLHRPWIPARRARKVFTVIEPVDINTPVLLAPQAGAQEKVDRSWYHNRGLVSLSAKIDRK

Parental  GYTPGEVIPVFAEIDNSSTHPVLPRAAVVQTQTFMARGARKQKQAVVASLAGEPVGPGQRVLWHGRALRI
          .YTPGEVIPVFA..DNSST.PVLPRA.VVQTQ.FMARGA.KQKQAVVA.LAGEPVGPGQR..W.GRALRI
Retrocopy SYTPGEVIPVFAKMDNSSTSPVLPRATVVQTQMFMARGA*KQKQAVVATLAGEPVGPGQRAVWQGRALRI

Parental  PPVGPSILHCRVLHVDYALKVCVDIPGTSKLLLELPLVIGTIPLHPFGSRSSSVGSHASFLLDWGPGALP
          PPVGPSILHCRVLHVDYALKVCVDI.GTSKLLLELPLVIGTIPLH.FGSRSSSVGSHASFLLD.G.GALP
Retrocopy PPVGPSILHCRVLHVDYALKVCVDILGTSKLLLELPLVIGTIPLHTFGSRSSSVGSHASFLLDLGLGALP

Parental  ERPE
          ERPE
Retrocopy ERPE

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	3.73 RPM
SRP051959_heart	0.04 RPM	5.89 RPM
SRP051959_kidney	0.00 RPM	4.15 RPM
SRP051959_liver	0.02 RPM	3.16 RPM
SRP051959_lung	0.00 RPM	11.11 RPM
SRP051959_lymph_node	0.02 RPM	29.59 RPM
SRP051959_skeletal_muscle	0.04 RPM	21.14 RPM
SRP051959_spleen	0.00 RPM	17.27 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1762 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1762 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1762 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010525	1 retrocopy	retro_cjac_560,
Callithrix jacchus	ENSCJAG00000036002	1 retrocopy	retro_cjac_1762 ,