RetrogeneDB - Retrocopy retro_pabe

						
>retro_pabe_3544
CTCCCGTCCACCGCCACCATGACCGCCAACGCACAGCCGAGGCAGTGCAGATCCAGTTCGGCCTCATCAACTGCGGCAAC

AAGTACCTGACGGCGGAGGCATTCGGGTTCAAGGTTAACGCGTTGGCCAGCAGCCTGAAGAAGCAGCAGATCTGGACGCC

GGAGCAGGCCCCTGATGAGGCGGGCAGCGCGGCCGTGTGCCTGCGCAGCCACCTGGGCCGCTACCTGGCGGCGGACAAGG

ACGGCAACGTGACCTGCGAGCGCGAGGTGCCCGGTCCCGACTGCCGCTTCCTCATCGTGGCGCACGACGACGGCCGCTGG

TCGCTGCAGTCCGAGGAGCACCGGCGCTACTTCGGAGGCACCGAGGACCGCCTGTCGTGCTTCGCGCAGACGGTGTCCCC

CGCCGAGAAGCGGAGCGTGCACATCGCCATGCACCCTCAGGTCAACATCTACAGCGTCACCCGTAGGCGCTAGGCGCACC

TGAGCCGGCGGCCGGCCGACGAGATCGCCGTGGACAGCGACGTGCCCTGGGGCATCCACTCGCTCATCATCCTCGCCTTC

CAGGACCAGCGCTACAGCGTGCAGACCGCCGACCACCGCTTCCTGCGCCATGACGGGCGCCTGGTGGCGAGCCCCGAGCT

GGCCACTGGCTACACGCTGGAGTTCCGCTTCGGCAAGGTGGCCTTCGGCGGCTGCGAGGGTCCTTACCTGGCGCCGTCGG

GGCCCAGCAGCACGCTCAAGGCCGGCAAGGCCACCAAGGCGGGCAAAGACGAGCTCTTTGCCCTGGAGCAGAGCTGCGCC

CAGGTCGTGCTGCAGGCGGCCAACGAGAGGAATGTGTCCACGCGCCAGGGTATGGACCTGTCTGCCAATCAGGACGAGGA

GACCGACCAGGAGACCTTCCAGCTGGAGATCGACTGCGACACCAAAAAGTGTGCCTTCCGTACCCACACGGGCAAGTACT

GGACGCTGACGGCCACTGGGGGCGTGCAGTCCACCGCCTCCACCCAGAATGTCAGCTGCTACTTCGACATTGAGCGGCGT

GACCGGCGCGTCACACTGCGGGCGTCCAATGGCAAGTTTGTGACATCTAAGAAGAATGGGCAGCTGGCCGCCTCGGTGGA

GACAGCAGGGGACTCA

ORF - retro_pabe_3544 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	92.37 %
Parental protein coverage:	85.36 %
Number of stop codons detected:	1
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalLSSTATMTANG-TAEAVQIQFGLINCGNKYLTAEAFGFKVNASASSLKKKQIWTLEQPPDEAGSAAVCLR
		L.STATMTAN..TAEAVQIQFGLINCGNKYLTAEAFGFKVNA.ASSLKK.QIWT.EQ.PDEAGSAAVCLR
RetrocopyLPSTATMTANA<TAEAVQIQFGLINCGNKYLTAEAFGFKVNALASSLKKQQIWTPEQAPDEAGSAAVCLR
ParentalSHLGRYLAADKDGNVTCEREVPGPDCRFLIVAHDDGRWSLQSEAHRRYFGGTEDRLSCFAQTVSPAEKWS
		SHLGRYLAADKDGNVTCEREVPGPDCRFLIVAHDDGRWSLQSE.HRRYFGGTEDRLSCFAQTVSPAEK.S
RetrocopySHLGRYLAADKDGNVTCEREVPGPDCRFLIVAHDDGRWSLQSEEHRRYFGGTEDRLSCFAQTVSPAEKRS
ParentalVHIAMHPQVNIYSVTRKRYAHLSARPADEIAVDRDVPWGVDSLITLAFQDQRYSVQTADHRFLRHDGRLV
		VHIAMHPQVNIYSVTR.R.AHLS.RPADEIAVD.DVPWG..SLI.LAFQDQRYSVQTADHRFLRHDGRLV
RetrocopyVHIAMHPQVNIYSVTRRR*AHLSRRPADEIAVDSDVPWGIHSLIILAFQDQRYSVQTADHRFLRHDGRLV
ParentalARPEPATGYTLEFRSGKVAFRDCEGRYLAPSGPSGTLKAGKATKVGKDELFALEQSCAQVVLQAANERNV
		A.PE.ATGYTLEFR.GKVAF..CEG.YLAPSGPS.TLKAGKATK.GKDELFALEQSCAQVVLQAANERNV
RetrocopyASPELATGYTLEFRFGKVAFGGCEGPYLAPSGPSSTLKAGKATKAGKDELFALEQSCAQVVLQAANERNV
ParentalSTRQGMDLSANQDEETDQETFQLEIDRDTKKCAFRTHTGKYWTLTATGGVQSTASTKNASCYFDIEWRDR
		STRQGMDLSANQDEETDQETFQLEID.DTKKCAFRTHTGKYWTLTATGGVQSTAST.N.SCYFDIE.RDR
RetrocopySTRQGMDLSANQDEETDQETFQLEIDCDTKKCAFRTHTGKYWTLTATGGVQSTASTQNVSCYFDIERRDR
ParentalRITLRASNGKFVTSKKNGQLAASVETAGDS
		R.TLRASNGKFVTSKKNGQLAASVETAGDS
RetrocopyRVTLRASNGKFVTSKKNGQLAASVETAGDS

							

							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	36 .22 RPM
SRP007412_cerebellum	0 .00 RPM	5 .84 RPM
SRP007412_heart	0 .00 RPM	0 .90 RPM
SRP007412_kidney	0 .00 RPM	4 .94 RPM
SRP007412_liver	0 .03 RPM	7 .04 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_3544 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3544 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_3544 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000075618	1 retrocopy	retro_hsap_1476,
Monodelphis domestica	ENSMODG00000001028	1 retrocopy	retro_mdom_423,
Ornithorhynchus anatinus	ENSOANG00000030243	1 retrocopy	retro_oana_11,
Pongo abelii	ENSPPYG00000017337	3 retrocopies	retro_pabe_1225, retro_pabe_3201, retro_pabe_3544 ,

	RetrogeneDB ID:	retro_pabe_3544
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	Un:16694437..16695573(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	FSCN1
	Ensembl ID:	ENSPPYG00000017337
	Aliases:	None
	Description:	fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus) [Source:HGNC Symbol;Acc:11148]

Parental	LSSTATMTANG-TAEAVQIQFGLINCGNKYLTAEAFGFKVNASASSLKKKQIWTLEQPPDEAGSAAVCLR
	L.STATMTAN..TAEAVQIQFGLINCGNKYLTAEAFGFKVNA.ASSLKK.QIWT.EQ.PDEAGSAAVCLR
Retrocopy	LPSTATMTANA<TAEAVQIQFGLINCGNKYLTAEAFGFKVNALASSLKKQQIWTPEQAPDEAGSAAVCLR

Parental	SHLGRYLAADKDGNVTCEREVPGPDCRFLIVAHDDGRWSLQSEAHRRYFGGTEDRLSCFAQTVSPAEKWS
	SHLGRYLAADKDGNVTCEREVPGPDCRFLIVAHDDGRWSLQSE.HRRYFGGTEDRLSCFAQTVSPAEK.S
Retrocopy	SHLGRYLAADKDGNVTCEREVPGPDCRFLIVAHDDGRWSLQSEEHRRYFGGTEDRLSCFAQTVSPAEKRS

Parental	VHIAMHPQVNIYSVTRKRYAHLSARPADEIAVDRDVPWGVDSLITLAFQDQRYSVQTADHRFLRHDGRLV
	VHIAMHPQVNIYSVTR.R.AHLS.RPADEIAVD.DVPWG..SLI.LAFQDQRYSVQTADHRFLRHDGRLV
Retrocopy	VHIAMHPQVNIYSVTRRR*AHLSRRPADEIAVDSDVPWGIHSLIILAFQDQRYSVQTADHRFLRHDGRLV

Parental	ARPEPATGYTLEFRSGKVAFRDCEGRYLAPSGPSGTLKAGKATKVGKDELFALEQSCAQVVLQAANERNV
	A.PE.ATGYTLEFR.GKVAF..CEG.YLAPSGPS.TLKAGKATK.GKDELFALEQSCAQVVLQAANERNV
Retrocopy	ASPELATGYTLEFRFGKVAFGGCEGPYLAPSGPSSTLKAGKATKAGKDELFALEQSCAQVVLQAANERNV

Parental	STRQGMDLSANQDEETDQETFQLEIDRDTKKCAFRTHTGKYWTLTATGGVQSTASTKNASCYFDIEWRDR
	STRQGMDLSANQDEETDQETFQLEID.DTKKCAFRTHTGKYWTLTATGGVQSTAST.N.SCYFDIE.RDR
Retrocopy	STRQGMDLSANQDEETDQETFQLEIDCDTKKCAFRTHTGKYWTLTATGGVQSTASTQNVSCYFDIERRDR

Parental	RITLRASNGKFVTSKKNGQLAASVETAGDS
	R.TLRASNGKFVTSKKNGQLAASVETAGDS
Retrocopy	RVTLRASNGKFVTSKKNGQLAASVETAGDS

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

RetrogeneDB ID:

retro_pabe_3544