RetrogeneDB ID: retro_ptro_469

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 10:10919440..10919788(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORMDL1
• Ensembl ID: ENSPTRG00000012736
• Aliases: None
• Description: None

Sequence

>retro_ptro_469
GTCTTACTCAGCATTCCTTCTTCCGTGTTCTCATTGCTTAGACCTTAACAAATATTATACATAATCTGGGATGAATGGAT
TTTTCCATGCTTGAAAGGAACACCTTTGGAAACCCCTGACCAGGGTAAAGCAAGGCTCCCAATGCACTGCGAACAACTGG
GTGATGGAGTACTGTTTACATCTTCACGGAAGTTTTTCACCCTTTCTCCAATCATTCTGTGTTTTCTAGCAAGTTTCTAT
AGAAGTATGCTCCAACTCACTCCATCGTAAGCACAGCTTCTCTCCTGAGTATGCTAAACTCCCCAAACGCAGCAACAACA
CAGTGTTCCGATCTTTGGAATTAATAAG

Alignment

ORF - retro_ptro_469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.31 %
• Parental protein coverage: 76.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VLLSIP-FFSVPVAWTLTNIIHNLG-MYVFLHA-VKGTPFETPDQGKARLLTHWEQLDYGVQFTSSRKFF
          VLLSIP.FF.V..A.TLTNIIHNLG.M..F.HA..KGTP.ETPDQGKARL..H.EQL..GV.FTSSRKFF
Retrocopy VLLSIP<FFRVLIA*TLTNIIHNLG<MNGFFHA<LKGTPLETPDQGKARLPMHCEQLGDGVLFTSSRKFF

Parental  TISPIILYFLASFYT-KYDPTHFILNTASLLSVL-IPKMPQLHGVRIFGINK
          T.SPIIL.FLASFY..KY.PTH.I..TASLLS.L..P...Q.H.V.IFGINK
Retrocopy TLSPIILCFLASFYR<KYAPTHSIVSTASLLSML>TPQTQQQHSVPIFGINK

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	0.02 RPM	25.52 RPM
SRP007412_cerebellum	0.00 RPM	20.97 RPM
SRP007412_heart	0.00 RPM	11.28 RPM
SRP007412_kidney	0.00 RPM	26.15 RPM
SRP007412_liver	0.00 RPM	12.14 RPM
SRP007412_testis	0.11 RPM	25.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_469 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_469 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_469 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_645
Gorilla gorilla	retro_ggor_565
Macaca mulatta	retro_mmul_2432

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005579	1 retrocopy	retro_cjac_2962,
Homo sapiens	ENSG00000128699	1 retrocopy	retro_hsap_645,
Gorilla gorilla	ENSGGOG00000015259	1 retrocopy	retro_ggor_565,
Loxodonta africana	ENSLAFG00000007769	1 retrocopy	retro_lafr_411,
Myotis lucifugus	ENSMLUG00000014339	1 retrocopy	retro_mluc_2318,
Macaca mulatta	ENSMMUG00000014316	1 retrocopy	retro_mmul_2432,
Nomascus leucogenys	ENSNLEG00000006625	1 retrocopy	retro_nleu_730,
Pongo abelii	ENSPPYG00000013017	2 retrocopies	retro_pabe_570, retro_pabe_571,
Pan troglodytes	ENSPTRG00000012736	1 retrocopy	retro_ptro_469 ,
Sus scrofa	ENSSSCG00000016044	1 retrocopy	retro_sscr_247,
Tupaia belangeri	ENSTBEG00000012942	1 retrocopy	retro_tbel_10,
Tursiops truncatus	ENSTTRG00000005240	2 retrocopies	retro_ttru_1846, retro_ttru_770,