RetrogeneDB ID: retro_pabe_3308

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:23134793..23135142(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJC5
• Ensembl ID: ENSPPYG00000011252
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily C, member 5 [Source:HGNC Symbol;Acc:16235]

Sequence

>retro_pabe_3308
GCAGACCAGAGACAGCGCTCACTGTCTACCTCTGGGGAATCATTGTACCACGTTCTTGGGCTGGACAAGAACGCAACCTC
AGATGACATTAAAAAGTCCTATCAGAAACTTGCCTTGAAATATCACTTTGACAAGAACCCTGACAACCCAGAGGCTGCAG
GCAAGTTTAAGGAGATCAACAAGGCCCACGCCAATCCTGACGGACACCACAAAAAGGAACATCTACGACAACTACGGCTC
GCTGGAGCTCTACCTGGCCAAACAGTTTGGGGAAGAGAACATGAACACCTACCTCGTGCTGTCCAGCGGGTGGGCCAAGG
CCCTGTTTGTCTTCTGCAGCCTCCTCACC

Alignment

ORF - retro_pabe_3308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.03 %
• Parental protein coverage: 69.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ADQRQRSLSTSGESLYHVLGLDKNATSDDIKKSYRKLALKYHPDKNPDNPEAADKFKEINNAHA-ILTDA
          ADQRQRSLSTSGESLYHVLGLDKNATSDDIKKSY.KLALKYH.DKNPDNPEAA.KFKEIN.AHA.ILTD.
Retrocopy ADQRQRSLSTSGESLYHVLGLDKNATSDDIKKSYQKLALKYHFDKNPDNPEAAGKFKEINKAHA>ILTDT

Parental  TKRNIYDKYGSLGLYVAEQFGEENVNTYFVLSSWWAKALFVFCGLLT
          TKRNIYD.YGSL.LY.A.QFGEEN.NTY.VLSS.WAKALFVFC.LLT
Retrocopy TKRNIYDNYGSLELYLAKQFGEENMNTYLVLSSGWAKALFVFCSLLT

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	0.77 RPM	46.22 RPM
SRP007412_cerebellum	0.36 RPM	23.59 RPM
SRP007412_heart	0.00 RPM	3.37 RPM
SRP007412_kidney	0.00 RPM	6.43 RPM
SRP007412_liver	0.00 RPM	2.48 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3308 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3308 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3308 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4028

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000101152	1 retrocopy	retro_hsap_4028,
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,