RetrogeneDB ID: retro_pabe_2136

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:82675902..82676921(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJB1
• Ensembl ID: ENSPPYG00000009647
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily B, member 1 [Source:HGNC Symbol;Acc:5270]

Sequence

>retro_pabe_2136
ATGGGCAAAGACAACTACCAGACGCTGGGCCTGGCCCGCGGCGCGTCGGACGAGGAGATCAAGCGGGCCTACAGCCGCCA
GGCGCTGCGCTACCACCCACACAAGAACAAGGAGCCTGGCGCCGAGGAGAAGTTCAAGGAGATCGCCGAGGCCTACGAGG
TGCTCAGAGACCCTCGCAAGCGCGAGATCTTCGACCACTACGCGGAGGAAGGCCTAAAGGGCAGCGGCCCCAGTGGCGGT
AGCGGCGGTGGTGCCAGTGCTACCTCTTTCAGCTACACATTCCGTGGAGACCCTCATGCCATGTTTGCTGAGTTCCGCGG
TGGCAGAAATCCCTCTGACACCTTTTTTGGGCAGCGGAACGGGGAGGAAGGCATGGACATTGCTGACCCATTCTCTGGCT
TCCCTATGGGAATGGGTGGCTTCACCAACATGAACTTTGGCCGCTCCCGCCCTGCCCAAGAGCCCACCCGAAAGAAGCAA
GATCCCCCAGGCACCCACAACCTTTGAGTCTCCCTTGAAGAGATCTACAGCAGTTGTACCAAGAGGATGAAAATCTCCCA
CAAGCGGCTAAACCCCGACAGAAAGAGCATTCGAAACGAAGACAAAATCTTGACCATTGAAGTGAAGAAGGGGTGGAAAG
AAGGGACCAAAATCACCTTCCCCAAAGAAGGAGACCAGACCTCCAACAACATTCCAGCCGATATCGTCTTTGTTTTAAAG
GACAAGCCACACAATATCTTTAAGAGAGATGGTTCTGATGTCATTTATCTTTCCAGAATCAGCCTCCCAGAGGCTCTGTG
TGGCCGCACAGTGAACGTCCCCACTCTGGACAGCAGGACCATACCCGTCGTGTTCAAAGATGCCATCAGGCCTGGCACGC
TGCGAAAAGTTCTGGAGAAGGCCTTCCCCTCCCCAAAACGCCAGAGAAACGTGGGGACCTCATTACTGAATTGGAAGTGA
TCTTCCCCGAAAGGATTCCCCAGACATCAAGAACCGTACTTGAGCAGATTCTTCCAGTA

Alignment

ORF - retro_pabe_2136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKEIAEAYDVLSDPRKREIFDRYGEE
          MGKD.YQTLGLARGASDEEIKRAY.RQALRYHP.KNKEPGAEEKFKEIAEAY.VL.DPRKREIFD.Y.EE
Retrocopy MGKDNYQTLGLARGASDEEIKRAYSRQALRYHPHKNKEPGAEEKFKEIAEAYEVLRDPRKREIFDHYAEE

Parental  GLKGSGPSGGSGGGANGTSFSYTFHGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSGFPMGMGG
          GLKGSGPSGGSGGGA..TSFSYTF.GDPHAMFAEF.GGRNP.DTFFGQRNGEEGMDI.DPFSGFPMGMGG
Retrocopy GLKGSGPSGGSGGGASATSFSYTFRGDPHAMFAEFRGGRNPSDTFFGQRNGEEGMDIADPFSGFPMGMGG

Parental  FTNVNFGRSRSAQEPARKKQDPPVTHDLRVSLEEIYSGCTKKMKISHKRLNPDGKSIRNEDKILTIEVKK
          FTN.NFGRSR.AQEP.RKKQDPP.TH.L.VSLEEIYS.CTK.MKISHKRLNPD.KSIRNEDKILTIEVKK
Retrocopy FTNMNFGRSRPAQEPTRKKQDPPGTHNL*VSLEEIYSSCTKRMKISHKRLNPDRKSIRNEDKILTIEVKK

Parental  GWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYPARISLREALCGCTVNVPTLDGRT
          GWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIY..RISL.EALCG.TVNVPTLD.RT
Retrocopy GWKEGTKITFPKEGDQTSNNIPADIVFVLKDKPHNIFKRDGSDVIYLSRISLPEALCGRTVNVPTLDSRT

Parental  IPVVFKDVIRPGMRRKV-PGEGLPLPKTPEKRGDLIIEFEVIFPERIPQTSRTVLEQVLPI
          IPVVFKD.IRPG..RKV..GEGLPLPKTPEKRGDLI.E.EVIFPERIPQTSRTVLEQ.LP.
Retrocopy IPVVFKDAIRPGTLRKV<SGEGLPLPKTPEKRGDLITELEVIFPERIPQTSRTVLEQILPV

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	0.00 RPM	89.35 RPM
SRP007412_cerebellum	0.12 RPM	93.51 RPM
SRP007412_heart	0.18 RPM	36.12 RPM
SRP007412_kidney	0.56 RPM	192.12 RPM
SRP007412_liver	0.34 RPM	96.52 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2136 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2136 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2136 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1728

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004666	1 retrocopy	retro_cjac_463,
Pongo abelii	ENSPPYG00000009647	1 retrocopy	retro_pabe_2136 ,
Pongo abelii	ENSPPYG00000011252	1 retrocopy	retro_pabe_3308,
Pongo abelii	ENSPPYG00000018228	4 retrocopies	retro_pabe_100, retro_pabe_2165, retro_pabe_226, retro_pabe_669,
Pan troglodytes	ENSPTRG00000010594	1 retrocopy	retro_ptro_1728,
Rattus norvegicus	ENSRNOG00000021824	1 retrocopy	retro_rnor_2233,