RetrogeneDB ID: retro_pabe_3272

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:87996589..87996899(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKFZP469K0627
• Ensembl ID: ENSPPYG00000014809
• Aliases: None
• Description: immunoglobulin J chain precursor [Source:RefSeq peptide;Acc:NP_001125381]

Sequence

>retro_pabe_3272
ATAAAGAACCATCTTCTTTTCTGGACAGTCCAGGCCATTTTTGTTAAGGCTGTTCTTGCTACACCAAGATGAAGATGAGA
GGATCATTCTTGTTGACGACAAATGTAAGTGGGCCCAGGTTATTTTCACCATCATCTCTTCTACCAAAGATCCTAATGAG
GACATTGCGGAGAGAAACATCCAAATTGCTGTTCTCCTGGACAACAAGAAGAATATCTCTGATCCCATCTCAAGGTTGAG
AACCAAATTTGTGTACCATTTGTCGTAACTCTGTAAAAAATGCGATCCTACGGAAGTGGAACTGGATAAT

Alignment

ORF - retro_pabe_3272 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.23 %
• Parental protein coverage: 64.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKNHLLFWGVLAIFIKAVHVKAQ-EDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNR
          .KNHLLFW.V.AIF.KAV......EDERI.LVD.KCK.A.....II.S..DPNEDI.ERNI.I.V.L.N.
Retrocopy IKNHLLFWTVQAIFVKAVLATPR>EDERIILVDDKCKWAQVIFTIISSTKDPNEDIAERNIQIAVLLDNK

Parental  ENISDPTSPLRTRFVYHLSDLCKKCDPTEVELDN
          .NISDP.S.LRT.FVYHLS.LCKKCDPTEVELDN
Retrocopy KNISDPISRLRTKFVYHLS*LCKKCDPTEVELDN

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	1.82 RPM
SRP007412_cerebellum	0.12 RPM	5.96 RPM
SRP007412_heart	0.00 RPM	1.08 RPM
SRP007412_kidney	0.00 RPM	24.99 RPM
SRP007412_liver	0.00 RPM	17.53 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3272 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3272 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3272 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2300

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014618	1 retrocopy	retro_cjac_1466,
Homo sapiens	ENSG00000132465	1 retrocopy	retro_hsap_4086,
Macaca mulatta	ENSMMUG00000022096	1 retrocopy	retro_mmul_2300,
Nomascus leucogenys	ENSNLEG00000007714	1 retrocopy	retro_nleu_3069,
Pongo abelii	ENSPPYG00000014809	1 retrocopy	retro_pabe_3272 ,
Pan troglodytes	ENSPTRG00000016134	1 retrocopy	retro_ptro_2771,