RetrogeneDB ID: retro_pabe_3708

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:139078513..139078993(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRD5A1
• Ensembl ID: ENSPPYG00000015333
• Aliases: None
• Description: steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1) [Source:HGNC Symbol;Acc:11284]

Sequence

>retro_pabe_3708
TTAATTTACCCATTTCTGATGCGAGGAGGAAAGCCTATGCCACTGTTGGCATGTACAATGGCGATTATGTTCTGTACCTG
TGATGGCTATTTGCAAAGCAGATACTTGAGCCATTGTGCAGTGTATGCTGATGACTGAGTAAAAGATCCCCGTTTTCTAA
TAAATTTTGGCTTGTGGTTAACGGACATGTTGATAAACATCCATTCAGATCATATCCTAAGGAATTTCAGAAAAACAGGA
GACACTGGATACAAAATACCAAGGGGAGGCTTATTTGAATACATAACTGCAGCCAACTATTTTGGAGAAATCATGGAGTG
GTGTGGCTATGCCCTGGCCAGCTGGTCTGTCCAAGGCGCGACTTTTGCTTTCTTCACATTTTGTTTTTTATCTGGTAGAG
CAAAAGAGCATCATGAGTGGTACCTCCGGAAATTTGAAGAGTATCCAAAGTTCAGAAAAATTATAATTCCATTTTTGTTT

Alignment

ORF - retro_pabe_3708 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.38 %
• Parental protein coverage: 95.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LIYPFLMRGGKPMPLLACTMAIMFCTCNGYLQSRYLSHCAVYADDWVTDPRFLIGFGLWLTGMLINIHSD
          LIYPFLMRGGKPMPLLACTMAIMFCTC.GYLQSRYLSHCAVYADD.V.DPRFLI.FGLWLT.MLINIHSD
Retrocopy LIYPFLMRGGKPMPLLACTMAIMFCTCDGYLQSRYLSHCAVYADD*VKDPRFLINFGLWLTDMLINIHSD

Parental  HILRNLRKPGDTGYKIPRGGLFEYVTAANYFGEIMEWCGYALASWSVQGAAFAFFTFCFLSGRAKEHHEW
          HILRN.RK.GDTGYKIPRGGLFEY.TAANYFGEIMEWCGYALASWSVQGA.FAFFTFCFLSGRAKEHHEW
Retrocopy HILRNFRKTGDTGYKIPRGGLFEYITAANYFGEIMEWCGYALASWSVQGATFAFFTFCFLSGRAKEHHEW

Parental  YLRKFEEYPKFRKIIIPFLF
          YLRKFEEYPKFRKIIIPFLF
Retrocopy YLRKFEEYPKFRKIIIPFLF

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	0.11 RPM	13.77 RPM
SRP007412_cerebellum	0.00 RPM	8.03 RPM
SRP007412_heart	0.00 RPM	0.21 RPM
SRP007412_kidney	0.07 RPM	3.05 RPM
SRP007412_liver	0.34 RPM	29.16 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3708 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3708 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3708 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4763
Gorilla gorilla	retro_ggor_2967

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005509	1 retrocopy	retro_chof_873,
Homo sapiens	ENSG00000145545	1 retrocopy	retro_hsap_4763,
Gorilla gorilla	ENSGGOG00000016593	1 retrocopy	retro_ggor_2967,
Nomascus leucogenys	ENSNLEG00000011414	1 retrocopy	retro_nleu_2347,
Pongo abelii	ENSPPYG00000015333	1 retrocopy	retro_pabe_3708 ,
Tursiops truncatus	ENSTTRG00000012679	1 retrocopy	retro_ttru_1340,