RetrogeneDB ID: retro_pabe_3134

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:41178057..41178678(-)
• Located in intron of: ENSPPYG00000017612

Retrocopy information

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

Parental gene information

• Parental gene symbol: STRAP
• Ensembl ID: ENSPPYG00000004334
• Aliases: None
• Description: serine/threonine kinase receptor associated protein [Source:HGNC Symbol;Acc:30796]

Sequence

>retro_pabe_3134
AAAGTGTGGGATGCTATCCCAGGAGATGAACTGATGACCCTGGCTCATAAACACATTATCAAGACTACGGATTTCATGCA
GGATAGTAATTATTTGTTAACCAGGGGACAGGATAAACCGTTTTGCATATATGACTTGAACAAACCTGAAGCAGAACCTG
AGGAAATTAGTGATCACAGCTCTGATATAAAAAAGGCCCTATGGTGCAGTAAAGATAAACAGATTCTTTCTTCTGATGAC
AAAACTGTTAGACTTTGGGATCATGCTACTATGACAGAAGTGAAATCTCTAAATTTTATTATGTTGGCTAGTAGTATGGA
ATATATTCCTGAGGGAGAGATTTTGATAATAACTTATGGCTGATCCAGTGCTTTTGACAGTACAGTAAGTTTGGAACCAA
TTAAATCCTTTCAAGCTCCTGCAACCATTAACTCTGAATCTCTTCACCTTGAGAAAGATTTTCTTGTTGCAGGTGGTGAA
GATGTTAAACTTGTAAGTAAGATGATAATAGTGGAGAAGAATTAGAATCCTATAAAGGGCACTCCGGTCCCATTCACTGT
GAGATTTGATCCTGATGGAGAACTCTATGCCAGTGGTTCTGAAGATGGAATACTGAGACTG

Alignment

ORF - retro_pabe_3134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 59.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVWDAVSGDELMTLAHKHIVKTVDFTQDSNYLLTGGQDKLLRIYDLNKPEAEPKEISGHTSGIKKALWCS
          KVWDA..GDELMTLAHKHI.KT.DF.QDSNYLLT.GQDK...IYDLNKPEAEP.EIS.H.S.IKKALWCS
Retrocopy KVWDAIPGDELMTLAHKHIIKTTDFMQDSNYLLTRGQDKPFCIYDLNKPEAEPEEISDHSSDIKKALWCS

Parental  EDKQILSADDKTVRLWDHATMTEVKSLNFNMSVSSMEYIPEGEILVITYGRSIAFHSAVSLDPIKSFEAP
          .DKQILS.DDKTVRLWDHATMTEVKSLNF.M..SSMEYIPEGEIL.ITYG.S.AF.S.VSL.PIKSF.AP
Retrocopy KDKQILSSDDKTVRLWDHATMTEVKSLNFIMLASSMEYIPEGEILIITYG*SSAFDSTVSLEPIKSFQAP

Parental  ATINSASLHPEKEFLVAGGEDFKLY-KYDYNSGEELESY-KGHFGPIHCVRFSPDGELYASGSEDGTLRL
          ATINS.SLH.EK.FLVAGGED.KL..K.D.NSGEELESY.KG...P...VRF.PDGELYASGSEDG.LRL
Retrocopy ATINSESLHLEKDFLVAGGEDVKLV<K*DDNSGEELESY>KGTPVPF-TVRFDPDGELYASGSEDGILRL

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	53.91 RPM
SRP007412_cerebellum	0.00 RPM	38.91 RPM
SRP007412_heart	0.03 RPM	32.03 RPM
SRP007412_kidney	0.03 RPM	35.73 RPM
SRP007412_liver	0.03 RPM	37.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3134 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3134 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3134 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3723
Pan troglodytes	retro_ptro_2616
Macaca mulatta	retro_mmul_1695

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007422	2 retrocopies	retro_chof_1098, retro_chof_1620,
Callithrix jacchus	ENSCJAG00000021593	1 retrocopy	retro_cjac_2503,
Homo sapiens	ENSG00000023734	2 retrocopies	retro_hsap_2092, retro_hsap_3723,
Gorilla gorilla	ENSGGOG00000009939	1 retrocopy	retro_ggor_1633,
Macaca mulatta	ENSMMUG00000013307	2 retrocopies	retro_mmul_1695, retro_mmul_985,
Mus musculus	ENSMUSG00000030224	1 retrocopy	retro_mmus_794,
Nomascus leucogenys	ENSNLEG00000004160	2 retrocopies	retro_nleu_1301, retro_nleu_1970,
Ochotona princeps	ENSOPRG00000015211	3 retrocopies	retro_opri_1029, retro_opri_217, retro_opri_541,
Pongo abelii	ENSPPYG00000001598	2 retrocopies	retro_pabe_3169, retro_pabe_3175,
Pongo abelii	ENSPPYG00000004334	3 retrocopies	retro_pabe_2005, retro_pabe_3134 , retro_pabe_3212,
Pan troglodytes	ENSPTRG00000004734	2 retrocopies	retro_ptro_1538, retro_ptro_2616,
Tursiops truncatus	ENSTTRG00000003466	2 retrocopies	retro_ttru_581, retro_ttru_974,