RetrogeneDB ID: retro_ptro_3200

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:41281399..41282305(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SDCBP
• Ensembl ID: ENSPTRG00000020277
• Aliases: SDCBP, syntenin-1
• Description: Pan troglodytes syndecan binding protein (syntenin) (SDCBP), mRNA. [Source:RefSeq mRNA;Acc:NM_001246446]

Sequence

>retro_ptro_3200
AAGAACCCTGCAAAAATGTCTCTCTATCCATCTCTTGAAAACTTGAAGGTAGACAAAGTAATTGGGGCTCAAACTACTTT
TTCTACAAACTCTGCCAATCCAGCAATTTTGTCAGAAGCTTCTGCTCCCATCTCTCAAAATGGAAATCTCTATCCCAAAT
TATATCCAGAGCTCTCTCAATACATGGGCCTGAGTTTAAATGAAGAAGAAATATGTGCAAATGTGGCCATGGTTTCTGGT
GCACCAATTCAGGGGCAGTTGGTAGCAAGACCTTCCAGTATGAACTATATGGTGGCTGCTGTAACTGGTAATGATGTTGG
AATTCACAGAGCAGAAATTAAGCAAGGGATTTGTGAAGTCATTTTGTGTAAGGATCACAATGGAAAAATTGGACTCAGGC
TTAAATCAATAGATAATGGTATATTTGTTCAGCTAGTCCAGGCTAATTCTCCAGCCTCATTGGTTGGTCTGAGAATTGAG
GACCAAGTACTCCAGATTAATAGTGAAAACTGTGCAGGGTAGAGCTCTGATAAAGCACACAAGGTGCTCAAACAGAATTT
TGGAGAGATTACCATGACCATTCATGACAGGCCGTTTGAATGGACGATTACCATGCATAAGGATAGCACTGGACATGTTG
GTTTTATCTTTAAAAATGGACAAATAACATCCATAGTGAAAGATAGCTCTGCAGCCAGAAATGGTCTTCTCACAGAACAT
AACATCTGTGAAATCAATGGACAGAATGTCATTGAATCGAAGGACTCTCAAACTGCAGACATACTGTCAACATCTGGGAC
TGTAGTTACTATTACAATCATGCCTGCTTTTATCTTTGAACATATTATTAAGCGGATGGCACCAAGCATTATGAAAAGCC
TAATGGACCACACCATTTCTGAGGTT

Alignment

ORF - retro_ptro_3200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.44 %
• Parental protein coverage: 94.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KNPAKMSLYPSLEDLKVDKVIQAQTAFSANPANPAILSEASAPIPHDGNLYPRLYPELSQYMGLSLNEEE
          KNPAKMSLYPSLE.LKVDKVI.AQT.FS.N.ANPAILSEASAPI...GNLYP.LYPELSQYMGLSLNEEE
Retrocopy KNPAKMSLYPSLENLKVDKVIGAQTTFSTNSANPAILSEASAPISQNGNLYPKLYPELSQYMGLSLNEEE

Parental  IRANVAVVSGAPLQG-LVARPSSINYMVAPVTGNDVGIRRAEIKQGIREVILCKDQDGKIGLRLKSIDNG
          I.ANVA.VSGAP.QG.LVARPSS.NYMVA.VTGNDVGI.RAEIKQGI.EVILCKD..GKIGLRLKSIDNG
Retrocopy ICANVAMVSGAPIQGQLVARPSSMNYMVAAVTGNDVGIHRAEIKQGICEVILCKDHNGKIGLRLKSIDNG

Parental  IFVQLVQANSPASLVGLRFGDQVLQINGENCAGWSSDKAHKVLKQAFGEKITMTIRDRPFERTITMHKDS
          IFVQLVQANSPASLVGLR..DQVLQIN.ENCAG.SSDKAHKVLKQ.FGE.ITMTI.DRPFE.TITMHKDS
Retrocopy IFVQLVQANSPASLVGLRIEDQVLQINSENCAG*SSDKAHKVLKQNFGE-ITMTIHDRPFEWTITMHKDS

Parental  TGHVGFIFKNGKITSIVKDSSAARNGLLTEHNICEINGQNVIGLKDSQIADILSTSGTVVTITIMPAFIF
          TGHVGFIFKNG.ITSIVKDSSAARNGLLTEHNICEINGQNVI..KDSQ.ADILSTSGTVVTITIMPAFIF
Retrocopy TGHVGFIFKNGQITSIVKDSSAARNGLLTEHNICEINGQNVIESKDSQTADILSTSGTVVTITIMPAFIF

Parental  EHIIKRMAPSIMKSLMDHTIPEV
          EHIIKRMAPSIMKSLMDHTI.EV
Retrocopy EHIIKRMAPSIMKSLMDHTISEV

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	0.04 RPM	56.39 RPM
SRP007412_cerebellum	0.00 RPM	35.60 RPM
SRP007412_heart	0.06 RPM	68.96 RPM
SRP007412_kidney	0.08 RPM	65.75 RPM
SRP007412_liver	0.13 RPM	52.05 RPM
SRP007412_testis	0.00 RPM	36.67 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3200 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3200 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4810
Gorilla gorilla	retro_ggor_2995
Pongo abelii	retro_pabe_3738
Macaca mulatta	retro_mmul_2564

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006161	1 retrocopy	retro_amel_654,
Bos taurus	ENSBTAG00000019910	2 retrocopies	retro_btau_1035, retro_btau_383,
Canis familiaris	ENSCAFG00000007112	1 retrocopy	retro_cfam_112,
Choloepus hoffmanni	ENSCHOG00000003565	5 retrocopies	retro_chof_1063, retro_chof_1151, retro_chof_1910, retro_chof_713, retro_chof_970,
Equus caballus	ENSECAG00000015053	1 retrocopy	retro_ecab_439,
Homo sapiens	ENSG00000137575	2 retrocopies	retro_hsap_3971, retro_hsap_4810,
Gorilla gorilla	ENSGGOG00000009019	2 retrocopies	retro_ggor_2666, retro_ggor_2995,
Loxodonta africana	ENSLAFG00000010757	1 retrocopy	retro_lafr_1044,
Microcebus murinus	ENSMICG00000003968	1 retrocopy	retro_mmur_170,
Myotis lucifugus	ENSMLUG00000004807	1 retrocopy	retro_mluc_12,
Macaca mulatta	ENSMMUG00000017296	1 retrocopy	retro_mmul_2564,
Mustela putorius furo	ENSMPUG00000010339	5 retrocopies	retro_mputfur_1055, retro_mputfur_1340, retro_mputfur_292, retro_mputfur_829, retro_mputfur_933,
Nomascus leucogenys	ENSNLEG00000001408	2 retrocopies	retro_nleu_2185, retro_nleu_2525,
Otolemur garnettii	ENSOGAG00000013462	1 retrocopy	retro_ogar_3259,
Procavia capensis	ENSPCAG00000016432	1 retrocopy	retro_pcap_186,
Pongo abelii	ENSPPYG00000018612	3 retrocopies	retro_pabe_3265, retro_pabe_3266, retro_pabe_3738,
Pan troglodytes	ENSPTRG00000020277	2 retrocopies	retro_ptro_2696, retro_ptro_3200 ,
Tupaia belangeri	ENSTBEG00000013965	1 retrocopy	retro_tbel_2142,