RetrogeneDB ID: retro_ptro_100

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL389461.1:5315..6080(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000039510
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAB41
• Ensembl ID: ENSPTRG00000021994
• Aliases: None
• Description: RAB41, member RAS oncogene family [Source:HGNC Symbol;Acc:18293]

Sequence

>retro_ptro_100
ATGTCCGCGGGCGGAGACCTCGGGAATCCGCTGAGGAAATTCAAGCTGGTGTTCCTGGGGGAGCAAAGCGTTGCAAAGAC
ATCTTTGATCACCAGATTCATGTATGACAGTTTTGACAACACCTATCAGGCAACAATTGGCATTGACTTTTTATCAAAAA
CTATGTACTTGGAGGATGGAACAATCGGGCTTCGGCTGTGGGATACGGCGGGTCAGGAACGTCTCCGTAGCCTCATTCCC
AGGTACATCCGTGATTCTGCTGCAGCTGTAGTAGTTTACGATATCACAAATGTTAACTCATTCCAGCAAACTACAAAGTG
GATTGATGATGTCAGAACAGAAAGAGGAAGTGATGTTATCATCACGCTAGTAGGAAATAGAACAGATCTTGCTGACAAGA
GGCAAGTGTCAATTGAGGAGGGAGAGAGGAAAGCCAAAGGGCTGAATGTTAGGTTTATTGAAACTAGGGCAAAAGCTGGA
TACAATGTAAAGCAGCTCTTTCGACGTGTAGCAGCAGCTTTGCCGGGAATGGAAAGCACACAGGACAGAAGCAGAGAAGA
CATGAGTGACATAAAACTGGAAAAGCCTCAGGAGCAACCAGTCAGCGAAGGGGGTTGTTCCTGCTACTCTCCCATGTCAT
CTTCAACCCTTCCTCAGAAGCCCCCTTACTCTTTCATTGACTGCAGTGTGAATATTGGCTTGAACCTTTTCCCTTCATTA
ATAACGTTTTGCAATTCATCATTGCTCCCTGTCTCGTGGAGATGA

Alignment

ORF - retro_ptro_100 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.77 %
• Parental protein coverage: 84.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LCKSKLLFLGEQSVGKTSIISRFMYNSFGCACQATVGIDFLSKTMYLEDQIVQLQLWDTAGQERFHSLIP
          L.K.KL.FLGEQSV.KTS.I.RFMY.SF....QAT.GIDFLSKTMYLED....L.LWDTAGQER..SLIP
Retrocopy LRKFKLVFLGEQSVAKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDGTIGLRLWDTAGQERLRSLIP

Parental  SYIRDSTIAVVVYDITNINSFKETDKWVEHV-AERGDDVVIMLLGNKIDFDNKRQVTAEQGEEKSRNLNV
          .YIRDS..AVVVYDITN.NSF..T.KW...V..ERG.DV.I.L.GN..D...KRQV..E.GE.K...LNV
Retrocopy RYIRDSAAAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIITLVGNRTDLADKRQVSIEEGERKAKGLNV

Parental  MFIETSAKTGYNVKKLFRRVASALLSTR-TSPPPKEGTVEIELESFEE
          .FIET.AK.GYNVK.LFRRVA.AL.....T.....E....I.LE...E
Retrocopy RFIETRAKAGYNVKQLFRRVAAALPGMESTQDRSREDMSDIKLEKPQE

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	2.25 RPM	3.99 RPM
SRP007412_cerebellum	0.32 RPM	2.29 RPM
SRP007412_heart	0.03 RPM	0.76 RPM
SRP007412_kidney	0.00 RPM	1.31 RPM
SRP007412_liver	0.13 RPM	0.13 RPM
SRP007412_testis	0.84 RPM	1.26 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_100 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_100 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_100 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000021994	1 retrocopy	retro_ptro_100 ,