RetrogeneDB ID: retro_ptro_2771

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:83098540..83098850(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IGJ
• Ensembl ID: ENSPTRG00000016134
• Aliases: None
• Description: immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides [Source:HGNC Symbol;Acc:5713]

Sequence

>retro_ptro_2771
ATAAAGAACTATCTTCTTTTCTGGACAGTCCAGGCCATTTTTGTTAAGGCTGTTCTTGTGACACCAGGATGAAGATGAGA
GGATCATTCTTGTTGATGACAAATATAAGTGGGCCCAGGTTATTTTCACCATCATCTCTTCTACCAAAGATCCTAATGAG
GGCATTGTGGAGAGAAACATCCAAATTGCTGTTCTCCTGGACAACAAGAAGAATATCTCTGATCCCATCTCAAGGTTGAG
AACCAAATTTGTGTACCATTTGTCATACCTCTGTAAAAAATGTGATCCTACAGAAGTGGAACTGGATAAT

Alignment

ORF - retro_ptro_2771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.27 %
• Parental protein coverage: 64.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKNHLLFWGVLAIFIKAVHVKA-QEDERIVLVDNKCKCARITSRIIRSSEDPNEDIVERNIRIIVPLNNR
          .KN.LLFW.V.AIF.KAV.V....EDERI.LVD.K.K.A.....II.S..DPNE.IVERNI.I.V.L.N.
Retrocopy IKNYLLFWTVQAIFVKAVLVTP>DEDERIILVDDKYKWAQVIFTIISSTKDPNEGIVERNIQIAVLLDNK

Parental  ENISDPTSPLRTRFVYHLSDLCKKCDPTEVELDN
          .NISDP.S.LRT.FVYHLS.LCKKCDPTEVELDN
Retrocopy KNISDPISRLRTKFVYHLSYLCKKCDPTEVELDN

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	0.16 RPM
SRP007412_cerebellum	0.00 RPM	0.11 RPM
SRP007412_heart	0.00 RPM	12.45 RPM
SRP007412_kidney	0.00 RPM	49.69 RPM
SRP007412_liver	0.00 RPM	5.70 RPM
SRP007412_testis	0.00 RPM	0.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2771 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2771 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2771 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4086

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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 ,