RetrogeneDB ID: retro_ptro_1728

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:196543400..196544416(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJB1
• Ensembl ID: ENSPTRG00000010594
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily B, member 1 [Source:HGNC Symbol;Acc:5270]

Sequence

>retro_ptro_1728
GTGGGCAAAGACTACTACCAGACGCTGGGCCTGGCCCGCGGCGCGTCAGACGAGGAGATCAAGCGGGCCTACCGCCGCCA
GGTGCTGCGCTACCACCCAGACAAGAACAAGGAGCCCGGCGCCGAGGAGAAGTTCAAGGAGATCGCCGAGGCCTATGAGG
TGCTCAGAGACCCGCGCAAGCGCGAGATCTTCGACCGCTACCGGGAGGAAGCCCTAAAGGGCAGCGGCCCCAGTGGCGGT
AGCGGCGGTGGTGCCAATGCTACCTCTTTCAGCTACACATTCCATGGAGACCCTCTTGCCATGTTTGCTGAGTTCTTCGG
TGGCAAAAATCCCTTTGACACCTTTTTTGGGCAGCGGAACGGGGAGGAAGTCATGGACATTGCTGACCCATTCTCTGGCT
TCCCTATGGGAATGGGTGGCTTCACCAACATGAACTTTGGCCGCTCCCGCCCTGCCCAGGAGCCCACCCGAAAGAAGCAA
GATCCCCCAGTCACCCACGACCTTCGAGTCTCCCTTGAAGAGATCTACAGCGGTTGTACCAAGAAGATGAAAATCTCCCA
CAAGCGGCTAAACCCCGACGGAAAGAGCATTCGAAACGAAGACAAAATCTTGACCATCGAAGTGAAGAAGGGGTGGAAAG
AAGGGACCAAGATCACCTTCCCCAAAGAAGGAGACCAGACCTCCAACAACATTCCAGCTGATATCGTCTTTGTTTTAAAG
GACAAGCCACACAATATCTTTAAGAGAGATGGTTCTGATGTCATTTATCCTTCCAGGATCAGCCTCCCGGAGGCTCTGTG
TGGCACACAGTGAACGTCCCCACTCTGGACGGCAGGACCATTCCCGTCGTGTTCAAAGATGCCATCAGGCCTGGCATGCG
ACGAAAAGTTCGTGGAGAAGGCCTTCCCCTCCCCAAAACGCCAGAGAAACGTGGGGACCTCATTATTGAATTGGAAGTGA
TCTTCCCCAAAAGGATTCCCCAGACATCAAGAACCGTACTTGAGCAGATTCTTCCA

Alignment

ORF - retro_ptro_1728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.94 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKREIFDRYR--
          .GKDYYQTLGLARGASDEEIKRAYRRQ.LRYHPDKNKEPGAEEKFKEIAEAY.VL.DPRKREIFDRYR..
Retrocopy VGKDYYQTLGLARGASDEEIKRAYRRQVLRYHPDKNKEPGAEEKFKEIAEAYEVLRDPRKREIFDRYREE

Parental  -LKGSGPSGGSGGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSGFPMGMGG
          .LKGSGPSGGSGGGAN.TSFSYTFHGDP.AMFAEFFGG.NPFDTFFGQRNGEE.MDI.DPFSGFPMGMGG
Retrocopy ALKGSGPSGGSGGGANATSFSYTFHGDPLAMFAEFFGGKNPFDTFFGQRNGEEVMDIADPFSGFPMGMGG

Parental  FTNVNFGRSRSAQEPARKKQDPPVTHDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKK
          FTN.NFGRSR.AQEP.RKKQDPPVTHDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKK
Retrocopy FTNMNFGRSRPAQEPTRKKQDPPVTHDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKK

Parental  GWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGC-TVNVPTLDGR
          GWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYP.RISL.EALCG..TVNVPTLDGR
Retrocopy GWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYPSRISLPEALCGT<TVNVPTLDGR

Parental  TIPVVFKDVIRPGMRRKVPGEGLPLPKTPEKRGDLIIEFEVIFPERIPQTSRTVLEQVLP
          TIPVVFKD.IRPGMRRKV.GEGLPLPKTPEKRGDLIIE.EVIFP.RIPQTSRTVLEQ.LP
Retrocopy TIPVVFKDAIRPGMRRKVRGEGLPLPKTPEKRGDLIIELEVIFPKRIPQTSRTVLEQILP

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
SRP007412_brain_prefrontal_cortex	0.14 RPM	61.18 RPM
SRP007412_cerebellum	0.04 RPM	44.77 RPM
SRP007412_heart	0.15 RPM	81.43 RPM
SRP007412_kidney	0.68 RPM	208.64 RPM
SRP007412_liver	0.36 RPM	164.91 RPM
SRP007412_testis	3.16 RPM	415.32 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1728 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1728 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1728 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_2136

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004666	1 retrocopy	retro_cjac_463,
Pongo abelii	ENSPPYG00000009647	1 retrocopy	retro_pabe_2136,
Pan troglodytes	ENSPTRG00000010594	1 retrocopy	retro_ptro_1728 ,
Rattus norvegicus	ENSRNOG00000021824	1 retrocopy	retro_rnor_2233,