RetrogeneDB ID: retro_ptro_798

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:131782765..131783719(-)
• Located in intron of: ENSPTRG00000005635

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRD5A3
• Ensembl ID: ENSPTRG00000016070
• Aliases: None
• Description: None

Sequence

>retro_ptro_798
ATGGCTCCCTGGGCGGAGGCCGAGCACTCGGCGCTGAACCCGCTGCGCGCGGTGTGGCTCACGCTGACCGCCGCCTTCCT
GCTGACCCTACTGCTGCAGCTCCTGCCGCCCGGCCTGCTCCCGGGCTGCGCGATCTTCCAGGACCTGATCCGCTATGGGA
AAACCAAGTGTGGGGAGCCGTCGCGCCCCGCCGCCTGCCGAGCCTTTGATGTCCCCAAGAGATATTTTTCCCACTTTTAT
ATCATCTCAGTGCTGTGGAATGGCTTCCTGCTTTGGTGCCTTACTCAATCTCTGTTCCTGGGAGCACCTTTTCCAAGCTG
GCTTCATGGTTTGCTCAGAATTCTCGGGGCGGCACAGTTCCAGGGAGGGGAGCTGGCACTGTCTGCATTCTTAGTGCTAG
TATTTCTGTGGCTGCACAGCTTACGAAGACTCTTCGAGTGCCTCTACGTCAGTGTCTTCTCCAATGTCATGATTCACGTC
GTGCAGTACTGTTTTGGACTTGTCTATTATGTCCTTGTTGGCCTAACTGTGCTGAGCCAAGTGCCAATGGATGGCAGGAA
TGCCTACATAACAGGGAAAAATCTATTGATGCAAGCACGGTGGTTCCATATTCTTGGGATGATGATGTTCATCTGGTCAT
CTGCCCATCAGTATAAGTGCCATGTTATTCTCGGCAATCTCAGGAAAAATAAAGCAGGAGTGGTCATTCACTGTAACCAC
ACGATCCCATTTGGAGACTGGTTTGAATATGTTTCTTCCCCTAACTACTTAGCAGAGCTGATGATCTACGTTTCCATGGC
TGTCACCTTTGGGTTCCACAACTTAACTTGGTGGCTAGTGGTGACAAATGTCTTCTTTAATCAGGCCCTGTCTGCCTTTC
TCAGCCACCAATTCTACAAAAGCAAATTTGTCTCTTACCCGAAGCATAGGAAAGCTTTCCTACCATTTTTGTTT

Alignment

ORF - retro_ptro_798 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPWAEAEHSALNPLRAVWLTLTAAFLLTLLLQLLPPGLLPGCAIFQDLIRYGKTKCGEPSRPAACRAFD
          MAPWAEAEHSALNPLRAVWLTLTAAFLLTLLLQLLPPGLLPGCAIFQDLIRYGKTKCGEPSRPAACRAFD
Retrocopy MAPWAEAEHSALNPLRAVWLTLTAAFLLTLLLQLLPPGLLPGCAIFQDLIRYGKTKCGEPSRPAACRAFD

Parental  VPKRYFSHFYIISVLWNGFLLWCLTQSLFLGAPFPSWLHGLLRILGAAQFQGGELALSAFLVLVFLWLHS
          VPKRYFSHFYIISVLWNGFLLWCLTQSLFLGAPFPSWLHGLLRILGAAQFQGGELALSAFLVLVFLWLHS
Retrocopy VPKRYFSHFYIISVLWNGFLLWCLTQSLFLGAPFPSWLHGLLRILGAAQFQGGELALSAFLVLVFLWLHS

Parental  LRRLFECLYVSVFSNVMIHVVQYCFGLVYYVLVGLTVLSQVPMDGRNAYITGKNLLMQARWFHILGMMMF
          LRRLFECLYVSVFSNVMIHVVQYCFGLVYYVLVGLTVLSQVPMDGRNAYITGKNLLMQARWFHILGMMMF
Retrocopy LRRLFECLYVSVFSNVMIHVVQYCFGLVYYVLVGLTVLSQVPMDGRNAYITGKNLLMQARWFHILGMMMF

Parental  IWSSAHQYKCHVILGNLRKNKAGVVIHCNHRIPFGDWFEYVSSPNYLAELMIYVSMAVTFGFHNLTWWLV
          IWSSAHQYKCHVILGNLRKNKAGVVIHCNH.IPFGDWFEYVSSPNYLAELMIYVSMAVTFGFHNLTWWLV
Retrocopy IWSSAHQYKCHVILGNLRKNKAGVVIHCNHTIPFGDWFEYVSSPNYLAELMIYVSMAVTFGFHNLTWWLV

Parental  VTNVFFNQALSAFLSHQFYKSKFVSYPKHRKAFLPFLF
          VTNVFFNQALSAFLSHQFYKSKFVSYPKHRKAFLPFLF
Retrocopy VTNVFFNQALSAFLSHQFYKSKFVSYPKHRKAFLPFLF

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	0.09 RPM	4.04 RPM
SRP007412_cerebellum	0.04 RPM	2.08 RPM
SRP007412_heart	0.00 RPM	1.40 RPM
SRP007412_kidney	0.03 RPM	1.94 RPM
SRP007412_liver	0.00 RPM	1.96 RPM
SRP007412_testis	0.11 RPM	4.00 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_798 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_798 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_798 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004093	1 retrocopy	retro_chof_1211,
Microcebus murinus	ENSMICG00000000317	1 retrocopy	retro_mmur_1071,
Pan troglodytes	ENSPTRG00000016070	1 retrocopy	retro_ptro_798 ,
Tursiops truncatus	ENSTTRG00000000958	1 retrocopy	retro_ttru_913,