RetrogeneDB ID: retro_pabe_1057

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13:66335428..66336017(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STAR
• Ensembl ID: ENSPPYG00000018520
• Aliases: None
• Description: steroidogenic acute regulatory protein [Source:HGNC Symbol;Acc:11359]

Sequence

>retro_pabe_1057
CTCAGCAACCAGGAGGGCTGGAAGAAGGAGAGCCAGCAGGACAATGGGGACAAAGTGAGGAGTAAAGTGGCTCCAGATGG
GGCAAGGTGTTCCGGCTGGAAGTCATGGTGGACCAGCCCATGGAAAGGCTCTACAAAGAGCTCGTGGACTGCATGGAGGC
AATGGGGGAGTGGAACTCCAATATCAAGGAGATCAAGGTCTTGCAGAAGATGATCAGAAAAGATACATTCATTGCCCATG
AGCTGGCTGCAGAGGCAGCAGGAAACCTAGTGGGGCCCCGTGACTTTGTGAGCATGTGCTGTGCCAAGCATCGAGGCTCC
ACCTGTGTGCTGGCTGGCATGGCCACAGACTTTGGGAACATGCCCGAGCAGAAGGGTGTCATCAGGGGGAGCATGGTCCC
ACTTGCATGGTGCTTCACCTGGTGACTGGAAGTCCCTCCAAGACCAAACTTATGTGACTGCTCAGCATCGACCTCAAGGG
GTGGCTGCCCAAGAACATCATCAATCAGGTCCTGTCCCAGACCCAGGTGGATTTTGCCAACCACCTGCACAAGCACCTGG
AGTCCCACCCTGCCTCTGAAGCCAGGTGT

Alignment

ORF - retro_pabe_1057 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.42 %
• Parental protein coverage: 68.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSNQEGWKKESQQDNGDKVMSKVVPDV-GKVFRLEVVVDQPMEMLYEELVERMEAMGEWNPSVKEIKVLQ
          LSNQEGWKKESQQDNGDKV.SKV.PD..GKVFRLEV.VDQPME.LY.ELV..MEAMGEWN...KEIKVLQ
Retrocopy LSNQEGWKKESQQDNGDKVRSKVAPDG<GKVFRLEVMVDQPMERLYKELVDCMEAMGEWNSNIKEIKVLQ

Parental  K-IGKDTFITHELAAEAAGNLVGPRDFVSVRCAKRRGSTCVLAGMATDFGNMPEQKGVIRA-EHGPTCMV
          K.I.KDTFI.HELAAEAAGNLVGPRDFVS..CAK.RGSTCVLAGMATDFGNMPEQKGVIR..EHGPTCMV
Retrocopy KMIRKDTFIAHELAAEAAGNLVGPRDFVSMCCAKHRGSTCVLAGMATDFGNMPEQKGVIRG<EHGPTCMV

Parental  LHPLAGSPSKTKLTWLLSIDLKGWLPKSIINQVLSQTQVDFANHLRKRLESRPVCEARC
          LH...GSPSKTKL..LLSIDLKGWLPK.IINQVLSQTQVDFANHL.K.LES.P..EARC
Retrocopy LHLVTGSPSKTKLM*LLSIDLKGWLPKNIINQVLSQTQVDFANHLHKHLESHPASEARC

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	1.33 RPM
SRP007412_cerebellum	0.00 RPM	1.58 RPM
SRP007412_heart	0.00 RPM	0.03 RPM
SRP007412_kidney	0.00 RPM	0.07 RPM
SRP007412_liver	0.00 RPM	0.46 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1057 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1057 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1057 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1273
Gorilla gorilla	retro_ggor_1000

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033345	3 retrocopies	retro_btau_1248, retro_btau_743, retro_btau_744,
Homo sapiens	ENSG00000147465	1 retrocopy	retro_hsap_1273,
Gorilla gorilla	ENSGGOG00000005787	1 retrocopy	retro_ggor_1000,
Pongo abelii	ENSPPYG00000018520	1 retrocopy	retro_pabe_1057 ,