RetrogeneDB ID: retro_ptro_753

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 12:36540018..36540903(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BTBD10
• Ensembl ID: ENSPTRG00000003377
• Aliases: None
• Description: None

Sequence

>retro_ptro_753
AGTACTTCCTCGCGTACTGCTAAAGGAGTCGACCACACCAAAATGAGTCTACATGATGCTAGTGGGGGACATAAGAGATC
AAGAGATAGATGAAGGTCAAGTGACAGATCACGAGATTCATCTCATGAAAGAACAGAGTCTCAACTCACTCCTTGTATTA
GAAATGTGACTTCTCCAACACAACAGCACCATGTTGAACAAGAAAAAGATTGCAGTTCCTCTCATCCAAGCAGTCTGCGT
CCTCAAAAAGCATCCCCAAATGGTTCCATTAGCAGTGCTGGGAACAGCAGCAGAAACAGTAGTCAGTCAAGTTCAGGTGG
TAGCTGTAAGACATCTGGGGAGATGGTGTTTGTATATGAAATTGCAAAAGAAGGAGCTCAGAATATAAGAATGTCAGAAC
GAGTGACACTAATAGTGGATAACACTAGATTTGTTGTAGACCCATCCATTTTTACTGCACAGCCAAATACAATGTTGGGC
AGGATGTTTGGATCTGGCCGAGAACATAACTTTACATGACCCAATAAGAAAGAAGAGTATGAGGTGGCAGAGGGGATTGG
TTCCACTGTGTTTTGAGCTATTCTGGATTACTATAAAACAGGAATAATCCATTGTCCTGATGGCATATCTATTCCTGAAG
TGAGAGAAGCATGTGACTGTCTTTGTATCTCTTTTGAATATAGTACTGTTAAATGTAGACATCTCAGTGCCCTAATGCAT
GAGTTATCAAATGATGGTGCTCATAGACAATCTGAATTTTATCTGGAAGAAATGATCCTTCCTCTCATGGTAGCTAGTGC
CCAGAGTGGGGAACGGGAATGTCATATAGTGGTGCTTACAGATGATAATGTGGTTGATTGGGATGAAGAATACCCACCAC
AGATG

Alignment

ORF - retro_ptro_753 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.88 %
• Parental protein coverage: 62.32 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  STSSRIAKGGVDHTKMSLHGASGGHERSRDRRRSSDRSRDSSHERTESQLTPCIRNVTSPTRQHHVEREK
          STSSR.AKG.VDHTKMSLH.ASGGH.RSRDR.RSSDRSRDSSHERTESQLTPCIRNVTSPT.QHHVE.EK
Retrocopy STSSRTAKG-VDHTKMSLHDASGGHKRSRDR*RSSDRSRDSSHERTESQLTPCIRNVTSPTQQHHVEQEK

Parental  DHSSSRPSSPRPQKASPNGSISSAGNSSRNSSQSSSDGSCKTAGEMVFVYENAKEGARNIRTSERVTLIV
          D.SSS.PSS.RPQKASPNGSISSAGNSSRNSSQSSS.GSCKT.GEMVFVYE.AKEGA.NIR.SERVTLIV
Retrocopy DCSSSHPSSLRPQKASPNGSISSAGNSSRNSSQSSSGGSCKTSGEMVFVYEIAKEGAQNIRMSERVTLIV

Parental  DNTRFVVDPSIFTAQPNTMLGRMFGSGREHNFTRPNEKGEYEVAEGIGSTVFRAILDYYKTGIIRCPDGI
          DNTRFVVDPSIFTAQPNTMLGRMFGSGREHNFT.PN.K.EYEVAEGIGSTVF.AILDYYKTGII.CPDGI
Retrocopy DNTRFVVDPSIFTAQPNTMLGRMFGSGREHNFT*PNKKEEYEVAEGIGSTVF*AILDYYKTGIIHCPDGI

Parental  SIPELREACDYLCISFEYSTIKCRDLSALMHELSNDGARRQFEFYLEEMILPLMVASAQSGERECHIVVL
          SIPE.REACD.LCISFEYST.KCR.LSALMHELSNDGA.RQ.EFYLEEMILPLMVASAQSGERECHIVVL
Retrocopy SIPEVREACDCLCISFEYSTVKCRHLSALMHELSNDGAHRQSEFYLEEMILPLMVASAQSGERECHIVVL

Parental  TDDDVVDWDEEYPPQM
          TDD.VVDWDEEYPPQM
Retrocopy TDDNVVDWDEEYPPQM

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	0.02 RPM	57.27 RPM
SRP007412_cerebellum	0.00 RPM	30.94 RPM
SRP007412_heart	0.00 RPM	12.07 RPM
SRP007412_kidney	0.00 RPM	9.65 RPM
SRP007412_liver	0.00 RPM	6.22 RPM
SRP007412_testis	0.00 RPM	107.17 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_753 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_753 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_753 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024984	1 retrocopy	retro_cpor_137,
Monodelphis domestica	ENSMODG00000008728	1 retrocopy	retro_mdom_1020,
Mus musculus	ENSMUSG00000038187	1 retrocopy	retro_mmus_3560,
Nomascus leucogenys	ENSNLEG00000017691	1 retrocopy	retro_nleu_232,
Otolemur garnettii	ENSOGAG00000000739	1 retrocopy	retro_ogar_3201,
Pan troglodytes	ENSPTRG00000003377	1 retrocopy	retro_ptro_753 ,
Rattus norvegicus	ENSRNOG00000014341	2 retrocopies	retro_rnor_2220, retro_rnor_2872,
Sorex araneus	ENSSARG00000000266	1 retrocopy	retro_sara_405,
Sus scrofa	ENSSSCG00000013395	2 retrocopies	retro_sscr_639, retro_sscr_640,
Tarsius syrichta	ENSTSYG00000000445	2 retrocopies	retro_tsyr_196, retro_tsyr_367,
Tursiops truncatus	ENSTTRG00000013943	1 retrocopy	retro_ttru_897,