RetrogeneDB ID: retro_cjac_2435

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:45739315..45740302(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000012255
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAK
• Ensembl ID: ENSCJAG00000001070
• Aliases: None
• Description: male germ cell-associated kinase [Source:HGNC Symbol;Acc:6816]

Sequence

>retro_cjac_2435
AAAAGTGAGGTTCATGAAATCTTTAAAATTTGCAAAGTTTTAGGGACTCCCAAAAAAGAGTGGCCAAAAGGATACCAGCT
GGCATCTTCTATGAATTTTCGTTTTCCCCAGTGTGTTCCTATAAACTTAAAAACTCTGATTCCCAATGCCAGTAATGAAG
CTATTCAGCTCATGACTGAAATGTTGAATTGGGATCCAATAAAACGACCAACAGCAAGCCGGGCATTGAAACACCCATAT
TTTCAAGTTGGTCAGGTATTAGGCCCTTCCTCAAATCATCTGGAATCAAAACGGTCTTTAAATAAGCAGCTGCAACCATT
AGAATCAAAGCCATCTTTAGTTGAAGTAGAGCCCAAGCCTCTACCAGATGTAATTGATCACACTGTTGGACAATCCCAGT
CGAAAACTAGCCAGCAGGCACTGCAGCCCATTCAGCCACCACAGAACTTGAGCGTCCAGCAACTACCAAAGCAACAGAAT
CAGCAGAAATCGCCACAAACACAATTCCCAAACATCATCAAAAACATGCCAACTAAGCCAAATGGCACACTGAATCATAA
AAGTGGTAGGAGGCATTGGGGCCAAACTAACTTCAAATCTGGAGAAAGCTGGGAAGAGTTGGAGGACTACGATTTCGGAG
CCTCCCATTCCAAGAAGCCAAGCATGGGTGTTTTTAAAGAAAAAAGGAAGAAAGAGTCTCCATTTCAGCTTCCAGAGCTG
GCATCCTTGGGCTCCAACCACTCGCTAGGGGAAAACAAGAGCTTACCTGCTGCTATTTCCCTAAAGTCTGATTCCGAATT
GTCAGCTGCTCCAGCTTCTAACCAGTACTACTTGAAACAATCAAGATATCTTCCAGGTGTGAATCCCAAGAACATGTCCT
TGATAGCCAGTGGAAAGGAAATAAACCCCCACACGTGGAGCAATCAGTTATTCCCTAAGTCACTGGGACCTGTCAGGGAA
GAACTTGCTTTCAAAAGGAGCAATGCA

Alignment

ORF - retro_cjac_2435 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.7 %
• Parental protein coverage: 53.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KSEVDEIFKICQVLGTSKKSDWPEGYQLASSMNFRFPQCIPINLKTLIPNASNEAIQLMTEMLNWDPMKR
          KSEV.EIFKIC.VLGT.KK..WP.GYQLASSMNFRFPQC.PINLKTLIPNASNEAIQLMTEMLNWDP.KR
Retrocopy KSEVHEIFKICKVLGTPKK-EWPKGYQLASSMNFRFPQCVPINLKTLIPNASNEAIQLMTEMLNWDPIKR

Parental  PRASQALKHTYFQVGQVLGPSSNHLESKQSLNTQLQPLESKPSLVEVEPKPLPDVIDQTVGQSQSKTSHQ
          P.AS.ALKH.YFQVGQVLGPSSNHLESK.SLN.QLQPLESKPSLVEVEPKPLPDVID.TVGQSQSKTS.Q
Retrocopy PTASRALKHPYFQVGQVLGPSSNHLESKRSLNKQLQPLESKPSLVEVEPKPLPDVIDHTVGQSQSKTSQQ

Parental  PLQPIQPPQNLSIQQPPKQQNQQKPPQTRFPNIIKNMPTKPNGTLNHKSGRRRWGQTIFKSGESWEEVED
          .LQPIQPPQNLS.QQ.PKQQNQQK.PQT.FPNIIKNMPTKPNGTLNHKSGRR.WGQT.FKSGESWEE.ED
Retrocopy ALQPIQPPQNLSVQQLPKQQNQQKSPQTQFPNIIKNMPTKPNGTLNHKSGRRHWGQTNFKSGESWEELED

Parental  YDFGASHSKKPSMGVFTEKRKKDSPSRPPELAPSGSNHLLGENKSLPAAISLKSDSELSTAPASKQYYLK
          YDFGASHSKKPSMGVF.EKRKK.SP...PELA..GSNH.LGENKSLPAAISLKSDSELS.APAS.QYYLK
Retrocopy YDFGASHSKKPSMGVFKEKRKKESPFQLPELASLGSNHSLGENKSLPAAISLKSDSELSAAPASNQYYLK

Parental  QSRYLPGVNPKNVSLIASGKEINPHTWSNQLFPKSLGPVREELAFKRSNA
          QSRYLPGVNPKN.SLIASGKEINPHTWSNQLFPKSLGPVREELAFKRSNA
Retrocopy QSRYLPGVNPKNMSLIASGKEINPHTWSNQLFPKSLGPVREELAFKRSNA

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	6.99 RPM
SRP051959_heart	0.00 RPM	10.44 RPM
SRP051959_kidney	0.02 RPM	10.87 RPM
SRP051959_liver	0.04 RPM	7.99 RPM
SRP051959_lung	0.31 RPM	14.79 RPM
SRP051959_lymph_node	0.02 RPM	7.83 RPM
SRP051959_skeletal_muscle	0.04 RPM	4.56 RPM
SRP051959_spleen	0.02 RPM	10.46 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2435 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2435 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2435 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001070	3 retrocopies	retro_cjac_1292, retro_cjac_2435 , retro_cjac_3002,