RetrogeneDB - Retrocopy retro_ptro

                        
>retro_ptro_705
ATGGAATTTCTGAAGACTTGTGTACTTAGAAGAAATGCGTGTACTGTGGTTTGCTTCTGGAGAAGCAAAGTTGTCCAAAG

GCCTTCCATTAGAAGGATTAGTACTACCTCTCCAAGGAGCACTGTCATGCCTGCTTGGGTGATAGATAAGTATGGGAAGA

ATGAAGTGCTTCGATTGACTCAGAACGTGATGATACCTATCATACGATATCCAAATGAAGTCATTGTAAAAGTTCACCCT

GCCAGTGTAAATCCTATAGACGTCAATATGAGAAGTGGTTATGGAGCTACAGCTTTAAATATGAAGCGTAATCCTTTACA

CATGAAAATCAAAGGAGAAGAATTTCCTCTGACTCTGATTCGGGATGTCTCTGGCATGGTGATGGAATGTGGGCTGGATG

TGAAGTACTTCAAGCCTTGAGATAAGGTCTGGGCTGCAGTTCCTCCTTGGAAACAAGGCACTCTTTCAGAGTTTGTTGTA

GTCAGTGGAAATGAGGTCTCTCACAAACCCAAATCACTCACTCATATATCAAGCTGCCTCTTCGCCATATGTGGCTCTCA

CAGCCTCATCTGCCATAAACAAAGTTGGTGACCTGAATGACAAGAATTGCACAGGAAGACATGTTCTAATCTTAGGCGCT

TCAGGCGGAGTTGGTGTTTTGCTATACAGGTAATGAAAGCATGGGATGCTCATGTGACAGCAGTTTGCGCTCAAGATGCC

AGTGAGCTTATAAAGAAGCTTGGGGCAGATGATGTAATTGATCACAAATTTGGAAGTGTGGAAGAGCAGTTGAAATCCTT

AAAACCGTTTGATTTCATCCTTGGTAATGTTGGCGGATCCACTAAAACATGGGCTCCAGATTTTCTCAAGAAATGGTCAG

GAGCCACCTATGTGACTTTGGTGAGTCCTTTCCTCCTGAACATGGACTGATTGGGCATAGCAGATGGCATGTTGCAGGCA

GGAGTCACCATAGGTTCGAAGGCATTAAAGCATTTCTGGAAAGGAGTCCATTATCGCTGGGCGTTTTTCATGGCC

ORF - retro_ptro_705 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	89.91 %
Parental protein coverage:	87.12 %
Number of stop codons detected:	2
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalMEFLKTCVLRRNACTAVCFWRSKVVQKPSVRRISTTSPRSTVMPAWVIDKYGKNEVLRFTQNMMMPIIHY
MEFLKTCVLRRNACT.VCFWRSKVVQ.PS.RRISTTSPRSTVMPAWVIDKYGKNEVLR.TQN.M.PII.Y
RetrocopyMEFLKTCVLRRNACTVVCFWRSKVVQRPSIRRISTTSPRSTVMPAWVIDKYGKNEVLRLTQNVMIPIIRY
ParentalPNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHMKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPG
PNEVIVKVH.ASVNPIDVNMRSGYGATALNMKR.PLHMKIKGEEFPLTL.RDVSG.VMECGLDVKYFKP.
RetrocopyPNEVIVKVHPASVNPIDVNMRSGYGATALNMKRNPLHMKIKGEEFPLTLIRDVSGMVMECGLDVKYFKP*
ParentalDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHT-QAASLPYVALTAWSAINKVGGLNDKNCTGKRVL
D.VWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTH..QAAS.PYVALTA.SAINKVG.LNDKNCTG..VL
RetrocopyDKVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHI>QAASSPYVALTASSAINKVGDLNDKNCTGRHVL
ParentalILGASGGVGT-FAVQVMKAWDAHVTAVCSQDASELVRKLGADDVIDYKSGSVEEQLKCLKPFDFILDNVG
ILGASGGVG..FA.QVMKAWDAHVTAVC.QDASEL..KLGADDVID.K.GSVEEQLK.LKPFDFIL.NVG
RetrocopyILGASGGVGV<FAIQVMKAWDAHVTAVCAQDASELIKKLGADDVIDHKFGSVEEQLKSLKPFDFILGNVG
ParentalGSTETWAPDFLKKWSGATYVTLVTPFLLNMDRLGIADGMLQTGVTVGSKALKHFWKGVHYRWAFFMA
GST.TWAPDFLKKWSGATYVTLV.PFLLNMD.LGIADGMLQ.GVT.GSKALKHFWKGVHYRWAFFMA
RetrocopyGSTKTWAPDFLKKWSGATYVTLVSPFLLNMD*LGIADGMLQAGVTIGSKALKHFWKGVHYRWAFFMA

                            

                            Legend:
                            
                                *Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

                        

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0 .00 RPM	5 .92 RPM
SRP007412_cerebellum	0 .00 RPM	8 .14 RPM
SRP007412_heart	0 .00 RPM	7 .08 RPM
SRP007412_kidney	0 .03 RPM	7 .51 RPM
SRP007412_liver	0 .00 RPM	3 .18 RPM
SRP007412_testis	0 .00 RPM	8 .96 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_705 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_705 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_705 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1030
Gorilla gorilla	retro_ggor_814
Pongo abelii	retro_pabe_863

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130347	1 retrocopy	retro_hsap_1030,
Gorilla gorilla	ENSGGOG00000008254	1 retrocopy	retro_ggor_814,
Nomascus leucogenys	ENSNLEG00000013349	1 retrocopy	retro_nleu_908,
Otolemur garnettii	ENSOGAG00000012703	1 retrocopy	retro_ogar_590,
Pongo abelii	ENSPPYG00000016882	1 retrocopy	retro_pabe_863,
Pan troglodytes	ENSPTRG00000018461	1 retrocopy	retro_ptro_705 ,

	RetrogeneDB ID:	retro_ptro_705
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	12:76034611..76035646(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	RTN4IP1
	Ensembl ID:	ENSPTRG00000018461
	Aliases:	None
	Description:	None

Parental	MEFLKTCVLRRNACTAVCFWRSKVVQKPSVRRISTTSPRSTVMPAWVIDKYGKNEVLRFTQNMMMPIIHY
	MEFLKTCVLRRNACT.VCFWRSKVVQ.PS.RRISTTSPRSTVMPAWVIDKYGKNEVLR.TQN.M.PII.Y
Retrocopy	MEFLKTCVLRRNACTVVCFWRSKVVQRPSIRRISTTSPRSTVMPAWVIDKYGKNEVLRLTQNVMIPIIRY

Parental	PNEVIVKVHAASVNPIDVNMRSGYGATALNMKRDPLHMKIKGEEFPLTLGRDVSGVVMECGLDVKYFKPG
	PNEVIVKVH.ASVNPIDVNMRSGYGATALNMKR.PLHMKIKGEEFPLTL.RDVSG.VMECGLDVKYFKP.
Retrocopy	PNEVIVKVHPASVNPIDVNMRSGYGATALNMKRNPLHMKIKGEEFPLTLIRDVSGMVMECGLDVKYFKP*

Parental	DEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHT-QAASLPYVALTAWSAINKVGGLNDKNCTGKRVL
	D.VWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTH..QAAS.PYVALTA.SAINKVG.LNDKNCTG..VL
Retrocopy	DKVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHI>QAASSPYVALTASSAINKVGDLNDKNCTGRHVL

Parental	ILGASGGVGT-FAVQVMKAWDAHVTAVCSQDASELVRKLGADDVIDYKSGSVEEQLKCLKPFDFILDNVG
	ILGASGGVG..FA.QVMKAWDAHVTAVC.QDASEL..KLGADDVID.K.GSVEEQLK.LKPFDFIL.NVG
Retrocopy	ILGASGGVGV<FAIQVMKAWDAHVTAVCAQDASELIKKLGADDVIDHKFGSVEEQLKSLKPFDFILGNVG

Parental	GSTETWAPDFLKKWSGATYVTLVTPFLLNMDRLGIADGMLQTGVTVGSKALKHFWKGVHYRWAFFMA
	GST.TWAPDFLKKWSGATYVTLV.PFLLNMD.LGIADGMLQ.GVT.GSKALKHFWKGVHYRWAFFMA
Retrocopy	GSTKTWAPDFLKKWSGATYVTLVSPFLLNMD*LGIADGMLQAGVTIGSKALKHFWKGVHYRWAFFMA

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_ptro_705