RetrogeneDB ID: retro_pabe_570

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 10:11301334..11301686(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ORMDL1
• Ensembl ID: ENSPPYG00000013017
• Aliases: None
• Description: ORM1-like protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q5R8X5]

Sequence

>retro_pabe_570
ATTGTCTTACTCAGCATTCCTTCGTCCGTGTTGTCATTGCTTACACCTTAATAAATATTATACACAATCTGGAAATGAAT
GGATTTTTCCATGCTTGAAAGGAGCACTGTTGGAAACCCCTGACCAGGGTAAAGCAAGGCTTCCAACGCACTGAGAACAA
GTGGGTGACAGAGTACCGTTTACGTCTTCATGGAAGTTTTTCACCATTTCTCCAACCATTCTACATTTTCCAGCAAGTTT
CTATAGAAGTATGCTCCAACTCACTCCATCGTAAGCACAGCTTCTCTCCTGAGTATGCTAAACTCCCCAAACGCCGCAAC
AACACAGCATTCCAATCTTTGGAATTAATAAG

Alignment

ORF - retro_pabe_570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.57 %
• Parental protein coverage: 77.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  IVLLSIP-FFSVPVAWTLTNIIHNLGMYVFLHA-VKGTPFETPDQGKARLLTHWEQLDYGVQFTSSRKFF
          IVLLSIP.F..V..A.TL.NIIHNL.M..F.HA..KG...ETPDQGKARL.TH.EQ....V.FTSS.KFF
Retrocopy IVLLSIP<FVRVVIAYTLINIIHNLEMNGFFHA<LKGALLETPDQGKARLPTH*EQVGDRVPFTSSWKFF

Parental  TISPIILYFLASFYT-KYDPTHFILNTASLLSVL-IPKMPQLHGVRIFGINK
          TISP.IL.F.ASFY..KY.PTH.I..TASLLS.L..P..PQ.H...IFGINK
Retrocopy TISPTILHFPASFYR<KYAPTHSIVSTASLLSML>TPQTPQQHSIPIFGINK

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	14.60 RPM
SRP007412_cerebellum	0.00 RPM	17.51 RPM
SRP007412_heart	0.00 RPM	7.86 RPM
SRP007412_kidney	0.00 RPM	10.67 RPM
SRP007412_liver	0.00 RPM	9.55 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_570 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_570 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_570 has 0 orthologous retrocopies within eutheria group .

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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,