RetrogeneDB - Retrocopy retro_pvam

                        
>retro_pvam_912
ATTGTTTTAAAAGCCCAGAAATTAGCTGGAGGAAGAGGAAAGGTAACTTCAGTAGCAGTTTGAAAGGAGACATTCATTTA

ACAAATACTCTAAAGTTGTAGGAAAGCTGGCTGAACAGATGATTAGGTATAACGTAGCAATAAAACAATTTCCAAAAGAA

CTAGAAGTTAATAAGGTGATGGTTGCTGAAGCCTTGGACATTTCCAGAGAAACCTACTTTGCGATTCTGATAGACTGGTC

CTGCAATGGCCCTGTCCTGATGGGCAGCCTCCAAAGGGGCGTTGACATTGAAGTGGTGGCAGCTTCAAACTCAGACCTTA

TTTTTAAAGAGCAAATTGACATTATTGAAGGGATAAAGGACAGTCAAGTTCAGCAGGTGGCAGAAATTCTAGTTTTTTGG

GGGGCCTTTGAAAAACCAGGCTGCAGATCAAGTTAAGAAGCTGTATTATCTCTTCCTGAAACTGATGCTACTCAGGTGGA

AGTGAACCCCTTTGGTGAAACTCCAGAAGGAACAAGTTTACCTCTGATGCCAAGATAAACTTTGATGACAACACAGAACT

TTGACAAAAGGACATATTTGCTTTGACTGACAAGTCAGAGAATGAGCCCATTGAAAATGAAACTGCCAGATATGAGACTA

AATAAATAGGGCTGGATGAGAACACTGCCTGCATTGTGAATTGGGCTGGACTCGCCATTGAGGCTTGTGATATAATTTTC

CTGAATGGTGAGAAACCAGCCAACTTCTTGGATCATGGTAATGGTGTAAAGGAAGCTCAAGTATATCAAGACTTTAAATT

GTTCACAGTTGAATCAATGGTTGAAGTAATCATTATTAATATTTTTGGTGGAATTATCAACTGTACCATCATTGTCAATG

AAATCACCAAAGCCTGCTGAGAGCTCAAACTTAAGGTGCCCCTGGTGATCTGGCTTGAGGGAACCAATGTCCACGAGGCC

CAGAAGATACTCAGTAATAGTGGGCTCCAAATACTTTGGCCATTGACCTGGAAGATGCAACCAATAAGGCTGTGGCCAGA

GTGGCTAAGAAG

ORF - retro_pvam_912 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	75.49 %
Parental protein coverage:	81.59 %
Number of stop codons detected:	3
Number of frameshifts detected:	6

Retrocopy - Parental Gene Alignment:

                                ParentalIVLKAQILAGGRGK-GIFSSGLKGGVHLT-KDPKVVGKLAKQMIGYNLATKQTPKEGVKVNKVMVAEALD
IVLKAQ.LAGGRGK.G.FSS.LKG..HLT.K..KVVGKLA.QMI.YN.A.KQ.PKE...VNKVMVAEALD
RetrocopyIVLKAQKLAGGRGK<GNFSSSLKGDIHLT<KYSKVVGKLAEQMIRYNVAIKQFPKE-LEVNKVMVAEALD
ParentalISRETYFAILMDRSYNGPVLVGSPQGGIDIEEVAASNPELIFKEQIDIIEGIKDSQAQRMAENLGFLG-P
ISRETYFAIL.D.S.NGPVL.GS.Q.G.DIE.VAASN..LIFKEQIDIIEGIKDSQ.Q..AE.L.F.G.P
RetrocopyISRETYFAILIDWSCNGPVLMGSLQRGVDIEVVAASNSDLIFKEQIDIIEGIKDSQVQQVAEILVFWG>P
ParentalLKNQAADQIKKLYNLFLKI-DATQVEVNPFGETPEGQVVCF-DAKINFDDNAEFRQKDIFAMDDKSENEP
LKNQAADQ.KKLY.LFLK..DATQVEVNPFGETPEG......DAKINFDDN.E..QKDIFA..DKSENEP
RetrocopyLKNQAADQVKKLYYLFLKL<DATQVEVNPFGETPEGTSLPL<DAKINFDDNTEL*QKDIFALTDKSENEP
Parental---EAARYDLKYIGLDGNIACFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKEAQVYQAFKLLTADPK
...E.ARY..K.IGLD.N.AC.VN.AGLA...CDIIFLNG.KPANFLD.G.GVKEAQVYQ.FKL.T....
RetrocopyIENETARYETK*IGLDENTACIVNWAGLAIEACDIIFLNGEKPANFLDHGNGVKEAQVYQDFKLFTVESM
ParentalVEAILVNIFGGIVNCAIIANGITKACRELELKVPLVIRLEGTNVHEAQKILSNSGL-PITSAIDLEDAAK
VE.I..NIFGGI.NC.II.N.ITKAC.EL.LKVPLVI.LEGTNVHEAQKILSNSGL.P.T.AIDLEDA..
RetrocopyVEVIIINIFGGIINCTIIVNEITKAC*ELKLKVPLVIWLEGTNVHEAQKILSNSGL<PNTLAIDLEDATN
ParentalKAVASVAKK
KAVA.VAKK
RetrocopyKAVARVAKK

                            

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

                        

RNA-Seq - click to see more details

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Pteropus vampyrus was not studied using ChIP-Seq data.

EST - click to see more details

Pteropus vampyrus was not studied using EST data.

TSS - click to see more details

Pteropus vampyrus was not studied using FANTOM5 data.

Lab - click to see more details

retro_pvam_912 was not experimentally validated.

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000172340	1 retrocopy	retro_hsap_1044,
Gorilla gorilla	ENSGGOG00000027438	1 retrocopy	retro_ggor_825,
Myotis lucifugus	ENSMLUG00000017294	1 retrocopy	retro_mluc_695,
Macaca mulatta	ENSMMUG00000009693	2 retrocopies	retro_mmul_1273, retro_mmul_1995,
Mus musculus	ENSMUSG00000061838	1 retrocopy	retro_mmus_3720,
Nomascus leucogenys	ENSNLEG00000007553	1 retrocopy	retro_nleu_915,
Otolemur garnettii	ENSOGAG00000006190	1 retrocopy	retro_ogar_161,
Pongo abelii	ENSPPYG00000013735	1 retrocopy	retro_pabe_2624,
Pteropus vampyrus	ENSPVAG00000004554	1 retrocopy	retro_pvam_912 ,

	RetrogeneDB ID:	retro_pvam_912
Retrocopy location	Organism:	*Megabat (Pteropus vampyrus)*
	Coordinates:	scaffold_16224:19594..20646(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	SUCLG2
	Ensembl ID:	ENSPVAG00000004554
	Aliases:	None
	Description:	succinate-CoA ligase, GDP-forming, beta subunit [Source:HGNC Symbol;Acc:11450]

Parental	IVLKAQILAGGRGK-GIFSSGLKGGVHLT-KDPKVVGKLAKQMIGYNLATKQTPKEGVKVNKVMVAEALD
	IVLKAQ.LAGGRGK.G.FSS.LKG..HLT.K..KVVGKLA.QMI.YN.A.KQ.PKE...VNKVMVAEALD
Retrocopy	IVLKAQKLAGGRGK<GNFSSSLKGDIHLT<KYSKVVGKLAEQMIRYNVAIKQFPKE-LEVNKVMVAEALD

Parental	ISRETYFAILMDRSYNGPVLVGSPQGGIDIEEVAASNPELIFKEQIDIIEGIKDSQAQRMAENLGFLG-P
	ISRETYFAIL.D.S.NGPVL.GS.Q.G.DIE.VAASN..LIFKEQIDIIEGIKDSQ.Q..AE.L.F.G.P
Retrocopy	ISRETYFAILIDWSCNGPVLMGSLQRGVDIEVVAASNSDLIFKEQIDIIEGIKDSQVQQVAEILVFWG>P

Parental	LKNQAADQIKKLYNLFLKI-DATQVEVNPFGETPEGQVVCF-DAKINFDDNAEFRQKDIFAMDDKSENEP
	LKNQAADQ.KKLY.LFLK..DATQVEVNPFGETPEG......DAKINFDDN.E..QKDIFA..DKSENEP
Retrocopy	LKNQAADQVKKLYYLFLKL<DATQVEVNPFGETPEGTSLPL<DAKINFDDNTEL*QKDIFALTDKSENEP

Parental	---EAARYDLKYIGLDGNIACFVNGAGLAMATCDIIFLNGGKPANFLDLGGGVKEAQVYQAFKLLTADPK
	...E.ARY..K.IGLD.N.AC.VN.AGLA...CDIIFLNG.KPANFLD.G.GVKEAQVYQ.FKL.T....
Retrocopy	IENETARYETK*IGLDENTACIVNWAGLAIEACDIIFLNGEKPANFLDHGNGVKEAQVYQDFKLFTVESM

Parental	VEAILVNIFGGIVNCAIIANGITKACRELELKVPLVIRLEGTNVHEAQKILSNSGL-PITSAIDLEDAAK
	VE.I..NIFGGI.NC.II.N.ITKAC.EL.LKVPLVI.LEGTNVHEAQKILSNSGL.P.T.AIDLEDA..
Retrocopy	VEVIIINIFGGIINCTIIVNEITKAC*ELKLKVPLVIWLEGTNVHEAQKILSNSGL<PNTLAIDLEDATN

Parental	KAVASVAKK
	KAVA.VAKK
Retrocopy	KAVARVAKK

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

RetrogeneDB ID:

retro_pvam_912