RetrogeneDB ID: retro_cjac_2931

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:114011567..114012465(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSPRY1
• Ensembl ID: ENSCJAG00000012138
• Aliases: None
• Description: ring finger and SPRY domain containing 1 [Source:HGNC Symbol;Acc:29420]

Sequence

>retro_cjac_2931
AGGGGCCGAGGACCACATGAGTCAAGGAGAAAGAAACAAAATGTGGATGGGCTAGTGTGGACACACTGGCAGTAATACGA
ACTCTGTAGATAATGATCAGGAACCTCCCTATTCCAATGATAACGTTACATGAAATGGCAGAAACAGATGAAGGATGGTT
GGATGTTGTCCAGTCTTTAATTAGAGTTATTCCACTGGAAGATCCATTGGGACCAGCTGTTATAACATTGTTACTAGATG
AATGTCCATTGCCCACTAAAGATGCACTCCAGAAATTGACTGAAATTCTCAATTTAAATGGAGAAGTAGCTTGCCAAGAC
TCAGGCCATCCTGCCAAACACAGGAACACATCTGCAGTCCTAAGGCTGCTTGGCAGAGAAACTAGCAGGTCCTGCAAATA
GGTTTACTTAGCCCAGGAATACTGGAATATTTGCTACAGTGTCTGAAGTTACAGTCCCACCCCACAGTCATGCTTTTTGC
ACTTATTGCACTGGAAAAGTTTGCACAGACAAGTGAAAATAAATTGACTATTTCTGAATCCAGTATTAGTGACCGGCTTG
TCACGTTGGAGTCCTGGGCTAATGATCCTGATTATCTGAAACATCAAGTTGGTTTCTGTGCCCAGTGGAGCTTAGACAAT
CTCTTTCTAAAAGAAGGTAGACAGCTGACCTATGAGAAAGTGAACTTGAGTAGCATTAGGGCCATGCTGAATAGCAATGA
CGTCAGCGAGTACCTGAAGATCTCACCTCATGGCTTAGAGGCTCGCTGTGATGCCTCCTCTTTTGAAAGTGTGCGTTGCA
CCTTTTGTGTGGATGCTGGGGTATGGTACTATGAAGTAACAATGGTCACTTCTGGCGTCATGCAGATTGGCTGGGCCACT
CGAGACAGCAAATTCCTC

Alignment

ORF - retro_cjac_2931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 52.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RGRGPHEPRRKKQNVDGLV-LDTLAVIRTL-VDNDQEPPYS-MITLHEMAETDEGWLDVVQSLIRVIPLE
          RGRGPHE.RRKKQNVDGLV..DTLAVIRTL.VDNDQEPPYS.MITLHEMAETDEGWLDVVQSLIRVIPLE
Retrocopy RGRGPHESRRKKQNVDGLV<VDTLAVIRTL<VDNDQEPPYS>MITLHEMAETDEGWLDVVQSLIRVIPLE

Parental  DPLGPAVITLLLDECPLPTKDALQKLTEILNLNGEVACQDSGHPAKHRNTSAVLGCLAEKLAGPAS-IGL
          DPLGPAVITLLLDECPLPTKDALQKLTEILNLNGEVACQDSGHPAKHRNTSAVL..L..........IGL
Retrocopy DPLGPAVITLLLDECPLPTKDALQKLTEILNLNGEVACQDSGHPAKHRNTSAVLRLLGRETSRSCK<IGL

Parental  LSPGILEYLLQCLKLQSHPTVMLFALIALEKFAQTSENKLTISESSISDRLVTLESWANDPDYLKRQVGF
          LSPGILEYLLQCLKLQSHPTVMLFALIALEKFAQTSENKLTISESSISDRLVTLESWANDPDYLK.QVGF
Retrocopy LSPGILEYLLQCLKLQSHPTVMLFALIALEKFAQTSENKLTISESSISDRLVTLESWANDPDYLKHQVGF

Parental  CAQWSLDNLFLKEGRQLTYEKVNLSSIRAMLNSNDVSEYLKISPHGLEARCDASSFESVRCTFCVDAGVW
          CAQWSLDNLFLKEGRQLTYEKVNLSSIRAMLNSNDVSEYLKISPHGLEARCDASSFESVRCTFCVDAGVW
Retrocopy CAQWSLDNLFLKEGRQLTYEKVNLSSIRAMLNSNDVSEYLKISPHGLEARCDASSFESVRCTFCVDAGVW

Parental  YYEVTVVTSGVMQIGWATRDSKFL
          YYEVT.VTSGVMQIGWATRDSKFL
Retrocopy YYEVTMVTSGVMQIGWATRDSKFL

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	0.07 RPM	18.95 RPM
SRP051959_heart	0.02 RPM	9.33 RPM
SRP051959_kidney	0.02 RPM	25.51 RPM
SRP051959_liver	0.04 RPM	12.30 RPM
SRP051959_lung	0.00 RPM	13.42 RPM
SRP051959_lymph_node	0.00 RPM	13.88 RPM
SRP051959_skeletal_muscle	0.00 RPM	6.27 RPM
SRP051959_spleen	0.00 RPM	13.78 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2931 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2931 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2931 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
Anolis carolinensis	ENSACAG00000006680	1 retrocopy	retro_acar_84,
Callithrix jacchus	ENSCJAG00000012138	1 retrocopy	retro_cjac_2931 ,