RetrogeneDB ID: retro_cjac_463

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:128031257..128032273(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022750
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DNAJB1
• Ensembl ID: ENSCJAG00000004666
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily B, member 1 [Source:HGNC Symbol;Acc:5270]

Sequence

>retro_cjac_463
ATGGGCAAAGACTACTCCCAGACGCTGGGCCTGGCCCGCGGCGCGTCGGACGAGGAGATCAAGCGGGCCTGCCGTCGCCA
GGCGCTGCGCTACCACCAGGACAAGAACAAGGGCCCGGCGCCGAGGAGAAGTTCAAGGAGATCGCCGAGGCCTACCACGT
GCTGAGCGAGCGCAAGCGCGAGATCTTCAACCGCTCCGGGGAGGAAGGGCTAAAGGGCAGCGGCCCCAGTGGCGGTAGCG
GTGGTGGTGCCAATGGTACCTCTTTCAGCTACACATTCCATGGAGACCCTCATGCCATGTCTGCTGAATTCTTCGGCGGC
AGAAATCCCTTTGACCCCTTTTTTGGGCAGCGGAACGGGGAGGAAGGCATGGACATTGACGACCCATTATCTGGCTTCCC
TATGGGCATGGGTGGCTTCACCAACATGAACTTTGGCGGCTCCCGCCCTGCCCAAGAGCTCACCCGAAAGAAGCAAGATC
CCCCAGTCACCCACGACCTTCGGGTCTCCCTTGAAGAGATCTACAGCAGCTGCACCAAGAAGATGAAAATCTCCCACAAG
CGGCTAAACTCCGATGAAAAGAGCATTCGAAACGAAGACAAAATCTTGACCATCGAAGTGAAGAAGGGGTGGAAAGAAGG
GACCAAAATCACATTCCCCAAGGAAGGAGACCAGACATCCAACAACATTCCAGATGATATTGTCTTTGTTTTAAAGGACA
AGCCGCACAATATCTTTAAGAGAGATGGCTCTGATGTCATTTATCCTGCCAGGATCAGCCTCCGGGAGGCTTTGTGTGGC
TGCACAGTGAACATCCCCACTCTGGACGGCAGGACCATACCCGTGCTATTCAAAGATGTCATCAGGCCTGGCATGCGTCG
AAAAGTTCCTGGAGAATGCCTCCCCCTCCCCAAAACGCCCGAGAAATGTGGGGACCTCATTACTGAGTTTGAAGTGATCT
TCCCCAAAAGGGTTCCCCAGACATCAAGATCCGCTCTTGAGAAGGTTCTTCCGATA

Alignment

ORF - retro_cjac_463 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKDYYQTLGLSRGASDEEIKRAYRRQALRYHPDKNKEP-GAEEKFKEIAEAYDVLSDPRKREIFDRYGE
          MGKDY.QTLGL.RGASDEEIKRA.RRQALRYH.DKNK.P.GAEEKFKEIAEAY.VLS..RKREIF.R.GE
Retrocopy MGKDYSQTLGLARGASDEEIKRACRRQALRYHQDKNKGP<GAEEKFKEIAEAYHVLSE-RKREIFNRSGE

Parental  EGLKGSGPRGGSGGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSGFHMGMG
          EGLKGSGP.GGSGGGANGTSFSYTFHGDPHAM.AEFFGGRNPFD.FFGQRNGEEGMDIDDP.SGF.MGMG
Retrocopy EGLKGSGPSGGSGGGANGTSFSYTFHGDPHAMSAEFFGGRNPFDPFFGQRNGEEGMDIDDPLSGFPMGMG

Parental  GFTNMNFGRSRPAQEPARKKQDPPVTHDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVK
          GFTNMNFG.SRPAQE..RKKQDPPVTHDLRVSLEEIYS.CTKKMKISHKRLN.D.KSIRNEDKILTIEVK
Retrocopy GFTNMNFGGSRPAQELTRKKQDPPVTHDLRVSLEEIYSSCTKKMKISHKRLNSDEKSIRNEDKILTIEVK

Parental  KGWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGCTVNVPTLDGR
          KGWKEGTKITFPKEGDQTSNNIP.DIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGCTVN.PTLDGR
Retrocopy KGWKEGTKITFPKEGDQTSNNIPDDIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGCTVNIPTLDGR

Parental  TIPVVFKDVIRPGMRRKVPGEGLPLPKTPEKRGDLIIEFEVIFPERIPQTSRSALEKVLPI
          TIPV.FKDVIRPGMRRKVPGE.LPLPKTPEK.GDLI.EFEVIFP.R.PQTSRSALEKVLPI
Retrocopy TIPVLFKDVIRPGMRRKVPGECLPLPKTPEKCGDLITEFEVIFPKRVPQTSRSALEKVLPI

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	0.93 RPM	60.95 RPM
SRP051959_heart	0.54 RPM	21.31 RPM
SRP051959_kidney	0.47 RPM	34.48 RPM
SRP051959_liver	0.93 RPM	52.57 RPM
SRP051959_lung	0.89 RPM	48.62 RPM
SRP051959_lymph_node	0.53 RPM	34.86 RPM
SRP051959_skeletal_muscle	0.28 RPM	23.54 RPM
SRP051959_spleen	1.09 RPM	51.87 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_463 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_463 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_463 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004666	1 retrocopy	retro_cjac_463 ,
Callithrix jacchus	ENSCJAG00000005288	7 retrocopies	retro_cjac_104, retro_cjac_1455, retro_cjac_1648, retro_cjac_1692, retro_cjac_2922, retro_cjac_3880, retro_cjac_948,
Pongo abelii	ENSPPYG00000009647	1 retrocopy	retro_pabe_2136,
Pan troglodytes	ENSPTRG00000010594	1 retrocopy	retro_ptro_1728,
Rattus norvegicus	ENSRNOG00000021824	1 retrocopy	retro_rnor_2233,