RetrogeneDB ID: retro_cjac_1508

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:35783021..35783732(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000032468
• Aliases: None
• Description: None

Sequence

>retro_cjac_1508
TATGAAATGCTGGACTTCCTTGGCTGTGGTGCCTTCGGTGAGGTCACACTGGCCCAGCGCTTGCTGACTAGGACCCAAGT
GGCGGTGAAAACCACCCTCAAAACTAGCTTCATCAGTAGCCACAGAGAGACGAGGATTTTAACGTCTGTGCACCACCCCA
ATATAATTAAACTATATCAAATTATTGACACCACAGAGGTGTGCCACTTGATCATGGAGTATGCATCAGGAGGAAGCCTG
TATGACTGGATTCAACACAACAATGTGATGGAGGAGGAGGCCTGAGCCATGTTCCAGCAGATGCTGTCCAGCATGAGGTA
CCTCCACAGAAAAAGAATAGCGCACAGAGACCTGAAACCGGAGAACATCCTCTTGGACGGTGAAGGAAATATAAAAATTG
CAGACTTTGGCTCAGCAACAACTTACTATGAGGGGCAGAGGCTGACAGTAGGTCATGGCACCCTCCTCTACATGGCCCCA
GAAGTCTTCCTGGGCCAGGGCTACTAATGCCCTGCCATGGATGATTGGAGCCTAGGTGTCACTTTGTTCGAGATGGTGTC
CAACACTCTGCCCTTCTTCTCAGAGAGTGCTATGCAACTCAAATCCATAATTAGATCTGGAAAGTACGTTTGCCCAGCCT
CCTTTTCAGAAGGCCTTAAAAGCCTAATGAAGAAACTCTTAACATCAGACCCAATGGAGTGGCCGACAGTA

Alignment

ORF - retro_cjac_1508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.6 %
• Parental protein coverage: 97.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YQILNFIGRGAFGEVTLARHLMTGTRVAVKTIDRTGFLSSHREMTVLQSVSHRNIIKLYHIINSKEACHF
          Y..L.F.G.GAFGEVTLA..L.T.T.VAVKT...T.F.SSHRE...L.SV.H.NIIKLY.II...E.CH.
Retrocopy YEMLDFLGCGAFGEVTLAQRLLTRTQVAVKTTLKTSFISSHRETRILTSVHHPNIIKLYQIIDTTEVCHL

Parental  VLEYAAGGSLSNWIERNIVEEEEARGMFQQMLSAVRYLHRRSIAHRDLKPDNMLLDVKGNIKIADFGSAT
          ..EYA.GGSL..WI..N.V.EEEA..MFQQMLS..RYLHR..IAHRDLKP.N.LLD..GNIKIADFGSAT
Retrocopy IMEYASGGSLYDWIQHNNVMEEEA*AMFQQMLSSMRYLHRKRIAHRDLKPENILLDGEGNIKIADFGSAT

Parental  SYHEGQRLTIAHGTLAYMAPELFGAQGYECPAMDIWSLGVTLFQMVSNNLPFFAVSRTQLKRLIHRAPSS
          .Y.EGQRLT..HGTL.YMAPE.F..QGY.CPAMD.WSLGVTLF.MVSN.LPFF..S..QLK..I......
Retrocopy TYYEGQRLTVGHGTLLYMAPEVFLGQGY*CPAMDDWSLGVTLFEMVSNTLPFFSESAMQLKSIIRSGKYV

Parental  VPGGLSVFTLAVLWLCRSSPPCPQPTL
          .P...S............S.P...PT.
Retrocopy CPASFSEGLKSLMKKLLTSDPMEWPTV

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	0.44 RPM
SRP051959_heart	0.09 RPM	0.63 RPM
SRP051959_kidney	0.80 RPM	0.64 RPM
SRP051959_liver	0.02 RPM	0.37 RPM
SRP051959_lung	0.02 RPM	0.93 RPM
SRP051959_lymph_node	0.02 RPM	1.42 RPM
SRP051959_skeletal_muscle	0.04 RPM	0.41 RPM
SRP051959_spleen	0.06 RPM	0.92 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1508 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1508 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1508 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032468	2 retrocopies	retro_cjac_1508 , retro_cjac_3847,