RetrogeneDB ID: retro_ptro_1379

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:57006452..57006766(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM50B
• Ensembl ID: ENSPTRG00000013869
• Aliases: None
• Description: Pan troglodytes transmembrane protein 50B (TMEM50B), mRNA. [Source:RefSeq mRNA;Acc:NM_001246571]

Sequence

>retro_ptro_1379
AGTGAGAGAAGAAATGTTGTGGCGTCTGTTGTGACAGGTATATTGTTTTTTACAGGCTGGTGGATAATGACGCAGCTGTG
GTGTATTGTAGGTCAGAACAGTTGAACCATGCCTTTCACACATGTGGTGTATTTCCCACATTGGCTTTCTTCATGATAAA
TGCTGTATCCAATGCTCAGGTGAGAGGTGATAGCTATGAAAGTGGCTGTATAGGAAGAACAGGTCCTTGAGTTTGGCTTT
TCGTTGGTTTCATGTTGATGTTTGGGGTACTTATTGCTTCCATGTGGATTCTTTTTGGTGCATATGTTACCCAA

Alignment

ORF - retro_ptro_1379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.05 %
• Parental protein coverage: 67.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SERRNAVASVVAGILFFTGWWIMI-DAAVVYPKPEQLNHAFHTCGVFSTLAFFMINAVSNAQVRGDSYES
          SERRN.VASVV.GILFFTG.W....DAAVVY...EQLNHAFHTCGVF.TLAFFMINAVSNAQVRGDSYES
Retrocopy SERRNVVASVVTGILFFTG-WWIM<DAAVVYCRSEQLNHAFHTCGVFPTLAFFMINAVSNAQVRGDSYES

Parental  GCLGRTGARVWLFIGFMLMFGSLIASMWILFGAYVTQ
          GC.GRTG..VWLF.GFMLMFG.LIASMWILFGAYVTQ
Retrocopy GCIGRTGP*VWLFVGFMLMFGVLIASMWILFGAYVTQ

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	0.55 RPM	14.14 RPM
SRP007412_cerebellum	0.61 RPM	34.02 RPM
SRP007412_heart	0.58 RPM	15.16 RPM
SRP007412_kidney	0.97 RPM	24.95 RPM
SRP007412_liver	0.16 RPM	11.36 RPM
SRP007412_testis	1.26 RPM	50.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1379 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1379 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2066
Gorilla gorilla	retro_ggor_1487
Pongo abelii	retro_pabe_1679
Macaca mulatta	retro_mmul_1408

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003928	1 retrocopy	retro_chof_422,
Gorilla gorilla	ENSGGOG00000034844	1 retrocopy	retro_ggor_1487,
Myotis lucifugus	ENSMLUG00000012388	1 retrocopy	retro_mluc_970,
Nomascus leucogenys	ENSNLEG00000003887	1 retrocopy	retro_nleu_2077,
Pan troglodytes	ENSPTRG00000013869	1 retrocopy	retro_ptro_1379 ,
Ictidomys tridecemlineatus	ENSSTOG00000023740	1 retrocopy	retro_itri_678,