RetrogeneDB ID: retro_cjac_414

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:74980105..74980825(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000031855
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PRR5
• Ensembl ID: ENSCJAG00000000538
• Aliases: None
• Description: None

Sequence

>retro_cjac_414
AGGAAGCTGCTGGACTCGCTGGCGGAGACCTGGGACTTCTTCTTCAGTTATGTGCTGCCCATGATGCAGGCCATCTTCTA
CCCGGTGCAGGGCAAGGAGCCGTCAGTGCGCCAGCTGGCCCTGCTGCACTTCCAGAATGCCATCACCCTCAGCATGAAGC
TAGAGGACGCACTGGCCCGGGCCCACGCCCGCGTGCCCCCTGCCATCGTGCAGATGCTGCTGGTGCTGCAGGGGGTGCAT
GAGTCCAGGGGAGTGACTAAGGACTACCTGCGCCTGGAGACGCTGGTCCAGAAGGTGGTATCGCCATACCTGGGCACCTA
CGGCCTCCACTCCAGCGAGGGGCCCTTCACCCACTCCTGCATCCTGGAAAAGCGCCTGCTGTGCCGCTCCCGCTCAGGGG
ACGTGCTGGCCAAGAACCCGGTGGTGCGTTCCAAGAGCTACACCACGCCGCTCCTGAACCCCGTGCAGGAGCACGAGGTG
GAGGGCACGGCGGCCGGCGGCACCAGCATCAGCAGGCACTCCGTGTCCGAGATGACTTCCTGCCCCGAGCCCCAGGGCTT
CTCCGACCTGCCTGGCCAGGGCCCCGCCGGAGCCTACAGGTCCTCCCCGGTGCCCCACTCAGGGCCATGCCCCAGCAGAC
TGCACCCCACGACCCAGCCCCCCGAGCAGGGCCCGGATCCCACCAGCAGCCCGCTGCCCGGCTCCAGCCCGGAGAACCTG

Alignment

ORF - retro_cjac_414 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 83.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QKLLDSLAETWDFFFSDVLPMLQAIFYPVQGKEPSVRQLALLHFRNAITLSVKLEDALARAHARVPPAIV
          .KLLDSLAETWDFFFS.VLPM.QAIFYPVQGKEPSVRQLALLHF.NAITLS.KLEDALARAHARVPPAIV
Retrocopy RKLLDSLAETWDFFFSYVLPMMQAIFYPVQGKEPSVRQLALLHFQNAITLSMKLEDALARAHARVPPAIV

Parental  QMLLVLQGVHESRGVTEDYLRLETLVQKVVSPYLGTYGLHSSEGPFTHSCILEKHLLRRSRSGDVLAKNP
          QMLLVLQGVHESRGVT.DYLRLETLVQKVVSPYLGTYGLHSSEGPFTHSCILEK.LL.RSRSGDVLAKNP
Retrocopy QMLLVLQGVHESRGVTKDYLRLETLVQKVVSPYLGTYGLHSSEGPFTHSCILEKRLLCRSRSGDVLAKNP

Parental  VVRSKSYNTPLLNPVQEHEAEGAAAGGTSIRRHSVSEMTSCPEPQGFSDLPGQGPAGACRSSPVPHSGPC
          VVRSKSY.TPLLNPVQEHE.EG.AAGGTSI.RHSVSEMTSCPEPQGFSDLPGQGPAGA.RSSPVPHSGPC
Retrocopy VVRSKSYTTPLLNPVQEHEVEGTAAGGTSISRHSVSEMTSCPEPQGFSDLPGQGPAGAYRSSPVPHSGPC

Parental  PSRLHPTTQPPEQGPDPTRSSLPGSSPENL
          PSRLHPTTQPPEQGPDPT.S.LPGSSPENL
Retrocopy PSRLHPTTQPPEQGPDPTSSPLPGSSPENL

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	1.46 RPM
SRP051959_heart	0.00 RPM	0.68 RPM
SRP051959_kidney	0.02 RPM	3.00 RPM
SRP051959_liver	0.00 RPM	2.60 RPM
SRP051959_lung	0.00 RPM	1.02 RPM
SRP051959_lymph_node	0.00 RPM	1.37 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.11 RPM
SRP051959_spleen	0.00 RPM	0.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_414 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_414 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_414 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000538	1 retrocopy	retro_cjac_414 ,