RetrogeneDB ID: retro_pabe_1429

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:5713468..5713900(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPSNAP1
• Ensembl ID: ENSPPYG00000011693
• Aliases: None
• Description: nipsnap homolog 1 (C. elegans) [Source:HGNC Symbol;Acc:7827]

Sequence

>retro_pabe_1429
CATGACAAGGAGTACCTGGAGGTCCGGAAGGAGTGTAGCTGGATGCTGTTGTCCAGGAGACACCAATTGCTCCTTGAGTT
CAGCTTCTGGAATGAGCCATAGCCCAGAGTAGACCCCAACATCTTATGAGCTGAGGACATGCCAGCTTAAGCTAGGAACC
ATGATGGAGTAGGGGAACAATTGGGGTCCTGCCAGCAGGTACCAGCAGCAAGTCCCAGCAGGAGAACCAGGAGGCGATGG
TGGCTTCTCCCAAATAGGAGAGCTCCACCTTGTGCATCATCTCTGGTCCTATAAAGACCCACAGTCTTGGGAGCAGACCC
GAAGTGCTGCCTGCAGGAAGAGGGCTTGGGATGAAATGTCTATTATACAGTTCTCCTGGTGCAACAGGTGGAGTCTTGGA
TCTGGGTCCTTTTGAAGACCTCACCTCTCCAG

Alignment

ORF - retro_pabe_1429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.07 %
• Parental protein coverage: 56.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NNKEYLEFRRERSQMLLSRRNQLLLEFSFWNEPQPRMGPNI-YELRTYKLKPGTMIEWGNNWARAIKYRQ
          ..KEYLE.R.E.S.MLLSRR.QLLLEFSFWNEP.PR..PNI.YELRT..LK.GTM.E.GNNW..A..Y.Q
Retrocopy HDKEYLEVRKECSWMLLSRRHQLLLEFSFWNEP*PRVDPNI>YELRTCQLKLGTMME*GNNWGPASRYQQ

Parental  E---NQEAVGGFFSQIGELYVVHHLWAYKDLQSREETRNAAWRKRGWDE-NVYYTVPLVRHMESRIMIPL
          ..........G.FSQIGEL..VHHLW.YKD.QS.E.TR.AA.RKR.WDE.NVYYTV.LV...ES.I...L
Retrocopy QVPAGEPGGDGGFSQIGELHLVHHLWSYKDPQSWEQTRSAACRKRAWDE<NVYYTVLLVQQVESWIWVLL

Parental  KISPLQ
          K.SPLQ
Retrocopy KTSPLQ

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	31.07 RPM
SRP007412_cerebellum	0.00 RPM	13.98 RPM
SRP007412_heart	0.00 RPM	1.57 RPM
SRP007412_kidney	0.00 RPM	37.99 RPM
SRP007412_liver	0.00 RPM	22.71 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1429 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1429 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1429 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_1211

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000031041	1 retrocopy	retro_mmul_1211,
Pongo abelii	ENSPPYG00000011693	1 retrocopy	retro_pabe_1429 ,
Tupaia belangeri	ENSTBEG00000004614	3 retrocopies	retro_tbel_247, retro_tbel_4673, retro_tbel_968,