RetrogeneDB ID: retro_pabe_3307

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 8:20480989..20481494(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM97
• Ensembl ID: ENSPPYG00000008086
• Aliases: None
• Description: transmembrane protein 97 [Source:HGNC Symbol;Acc:28106]

Sequence

>retro_pabe_3307
TGCATGGAGTGGCTGCTGGGCTTCTACTTCCTCAGCCACATCCCCATCACCCTGTTCATGGACCTGTAGGCAGTGCTGCC
GTGCGAGCTCTACCCAGCAGAATTTAGAAACCTGCTGAAGTGCTATGCTAAGGAGTTCAAAGACCCACTGCTACAGGAGC
CACCAGCCTGGTTTAAGTCCTTTCTGTTTTGCAAGCTTGTGTTTCAGGTGCCTTTCTTTCCCATTGCAACCTATGCCTTC
CTCAAAGGAAGCTGCAAGTGGATTTGAACCCCTGCAAATCATCTACTCAGTTCATACCATGATGACTTTAATTCCGCTAC
TCTCCACATTTCTGTTTGAGGATTTCTCCAAAGCCAGTTGTTTCCAAGGATAAAGACCTGAGACTCTGCATAAACGGTTA
ACCCCTGTATCTGTCTATGCCCCATACTTACTCATCCCAGTCTTACTTTTAATTTTCATGTTGCAGAGCCCCCACTACAA
GTATGAGGAGAAAAGAAAAAAGAAA

Alignment

ORF - retro_pabe_3307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.98 %
• Parental protein coverage: 69.14 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CVEWLLGLYFLSHIPITLFMDLQAVLPRELYPVEFRNLLKWYAKEFKDPLLQEPPAWFKSFLFCELVFQL
          C.EWLLG.YFLSHIPITLFMDL.AVLP.ELYP.EFRNLLK.YAKEFKDPLLQEPPAWFKSFLFC.LVFQ.
Retrocopy CMEWLLGFYFLSHIPITLFMDL*AVLPCELYPAEFRNLLKCYAKEFKDPLLQEPPAWFKSFLFCKLVFQV

Parental  PFFPIATYAFLKGSCKWIRTPA-IIYSVHTMTTLIPILSTFLFEDFSKASGFKGQRPETLHERLTLVSVY
          PFFPIATYAFLKGSCKWI.TPA.IIYSVHTM.TLIP.LSTFLFEDFSKAS.F.G.RPETLH.RLT.VSVY
Retrocopy PFFPIATYAFLKGSCKWI*TPA>IIYSVHTMMTLIPLLSTFLFEDFSKASCFQG*RPETLHKRLTPVSVY

Parental  APYLVIPFVLLIFMLRSPYYKYEEKRKKK
          APYL.IP..LLIFML.SP.YKYEEKRKKK
Retrocopy APYLLIPVLLLIFMLQSPHYKYEEKRKKK

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	0.77 RPM
SRP007412_cerebellum	0.00 RPM	0.36 RPM
SRP007412_heart	0.00 RPM	0.15 RPM
SRP007412_kidney	0.00 RPM	0.43 RPM
SRP007412_liver	0.00 RPM	4.77 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3307 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3307 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3307 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4027
Pan troglodytes	retro_ptro_2731
Gorilla gorilla	retro_ggor_2703
Macaca mulatta	retro_mmul_2323

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011105	1 retrocopy	retro_chof_566,
Homo sapiens	ENSG00000109084	1 retrocopy	retro_hsap_4027,
Gorilla gorilla	ENSGGOG00000004565	1 retrocopy	retro_ggor_2703,
Macaca mulatta	ENSMMUG00000019142	1 retrocopy	retro_mmul_2323,
Mus musculus	ENSMUSG00000037278	1 retrocopy	retro_mmus_1451,
Nomascus leucogenys	ENSNLEG00000001868	1 retrocopy	retro_nleu_1574,
Otolemur garnettii	ENSOGAG00000003329	1 retrocopy	retro_ogar_1913,
Pongo abelii	ENSPPYG00000008086	1 retrocopy	retro_pabe_3307 ,
Pan troglodytes	ENSPTRG00000008909	1 retrocopy	retro_ptro_2731,
Ictidomys tridecemlineatus	ENSSTOG00000007542	2 retrocopies	retro_itri_341, retro_itri_758,
Tupaia belangeri	ENSTBEG00000005125	2 retrocopies	retro_tbel_2160, retro_tbel_2221,