RetrogeneDB - Retrocopy retro_pvam

                        
>retro_pvam_1198
GAAGTGAGACAGACCAAAGAATAAGCCAGTGAGGAGATTTTGGAAGCAGAACAGAAACGTAACAAACTGCCAACCATTTT

TTTCAAGAGGTCGGAATTAATTGCACAAATCCAATTTTGCTGTAACTCTGTCAACCATCATCAAGGGTCTGCACTGCTTA

GGGAGGAGGATGACGAGGGACTGCATTGTATGACAAAAGTTGACACGACAGAATTTTAAGATGTTAAGATCATTTACAAA

GTAGATTTTTATTTTGATGAAAAGCCTTACTTTGAAAGTCATGTTTCCTCTTCAGAATTTCATCTGATTGAGAGTGGTGA

TTCATCTTCAAAGTCCACTGAAATCAAATGGAAATCTAAGAAGGATTCAATGAAACGTTCAAGTCCAACATAGAATAAAG

CCAATAGGCGCAGACATTATGAGGAACCAGGGACATACTTACCTGGCTTACTGACCATTCTGATACATGTGCAGATGAGT

TAGGAAAAGTCCTCAAAGATGATATTTGGCCAAGTCTATTACGATACCATTTGGTTCCTGACATGTATGATGAAGGAGAA

GAAGAAGGTGATAATATGGTAGAAGAAAGATTGGAAGTTATTGATGAAGAAGCAGATGAGGATGAAAGTGAATTAGGTGA

AGATGATGATGAGGTGGGGAAGGATAGAAAAGGAACACGGATGAT

ORF - retro_pvam_1198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	61.34 %
Parental protein coverage:	81.66 %
Number of stop codons detected:	4
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalEIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEALHYLTRV
E.....E.ASEEIL..EQK.NKL...FF.KRSELIA.I........VNH.Q.SALL.EED.E.LH..T.V
RetrocopyEVRQTKE*ASEEILEAEQKRNKLPTIFF-KRSELIAQIQ--FCCNSVNHHQGSALLREEDDEGLHCMTKV
ParentalEVTEFEDIKSGYRIDFYFDENPYFENKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRSSQTQNKASRK
..TEF.D.K..Y..DFYFDE.PYFE..V.S.EFHL.ESGD.SSKSTEIKWKS.KD..KRSS.T.NKA.R.
RetrocopyDTTEF*DVKIIYKVDFYFDEKPYFESHVSSSEFHLIESGDSSSKSTEIKWKSKKDSMKRSSPT*NKANRR
ParentalRQHEEPESF-FTWFTDHSDAGADELGEVIKDDIWPNPLQYYLVPDMDDEEGEGEEDDDDDEEEEGLEDID
R..EEP.....TW.TDHSD..ADELG.V.KDDIWP..L.Y.LVPDM.DE...GEE..D...EE..LE.ID
RetrocopyRHYEEPGTY<LTWLTDHSDTCADELGKVLKDDIWPSLLRYHLVPDMYDE---GEEEGDNMVEER-LEVID
ParentalEEGDEDEGEEDEDDDE-GEEGEEDEGED
EE.DEDE.E..EDDDE.G.EG......D
RetrocopyEEADEDESELGEDDDE<GGEG*KRNTDD

                            

                            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_1198 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 16 parental genes, and 136 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015686	7 retrocopies	retro_amel_1093, retro_amel_1201, retro_amel_1459, retro_amel_1675, retro_amel_530, retro_amel_631, retro_amel_634,
Bos taurus	ENSBTAG00000020959	8 retrocopies	retro_btau_1179, retro_btau_1490, retro_btau_1519, retro_btau_1556, retro_btau_464, retro_btau_469, retro_btau_749, retro_btau_955,
Canis familiaris	ENSCAFG00000032728	2 retrocopies	retro_cfam_47, retro_cfam_83,
Felis catus	ENSFCAG00000005848	2 retrocopies	retro_fcat_130, retro_fcat_89,
Microcebus murinus	ENSMICG00000017643	2 retrocopies	retro_mmur_1398, retro_mmur_775,
Myotis lucifugus	ENSMLUG00000014291	13 retrocopies	retro_mluc_1026, retro_mluc_1120, retro_mluc_1673, retro_mluc_1977, retro_mluc_2098, retro_mluc_2188, retro_mluc_2361, retro_mluc_2412, retro_mluc_2584, retro_mluc_419, retro_mluc_524, retro_mluc_855, retro_mluc_881,
Mustela putorius furo	ENSMPUG00000013069	10 retrocopies	retro_mputfur_1330, retro_mputfur_1556, retro_mputfur_1581, retro_mputfur_1605, retro_mputfur_221, retro_mputfur_274, retro_mputfur_286, retro_mputfur_723, retro_mputfur_785, retro_mputfur_799,
Mus musculus	ENSMUSG00000054766	17 retrocopies	retro_mmus_1366, retro_mmus_1435, retro_mmus_1671, retro_mmus_1743, retro_mmus_2329, retro_mmus_2448, retro_mmus_2484, retro_mmus_2664, retro_mmus_2665, retro_mmus_3015, retro_mmus_3290, retro_mmus_345, retro_mmus_3513, retro_mmus_517, retro_mmus_887, retro_mmus_929, retro_mmus_967,
Nomascus leucogenys	ENSNLEG00000017595	2 retrocopies	retro_nleu_108, retro_nleu_870,
Oryctolagus cuniculus	ENSOCUG00000007501	12 retrocopies	retro_ocun_1107, retro_ocun_1110, retro_ocun_1234, retro_ocun_1311, retro_ocun_1563, retro_ocun_276, retro_ocun_407, retro_ocun_421, retro_ocun_423, retro_ocun_476, retro_ocun_859, retro_ocun_923,
Otolemur garnettii	ENSOGAG00000007635	13 retrocopies	retro_ogar_115, retro_ogar_1370, retro_ogar_3084, retro_ogar_3186, retro_ogar_3195, retro_ogar_3289, retro_ogar_447, retro_ogar_465, retro_ogar_543, retro_ogar_565, retro_ogar_806, retro_ogar_899, retro_ogar_934,
Pongo abelii	ENSPPYG00000019659	17 retrocopies	retro_pabe_1076, retro_pabe_1110, retro_pabe_1150, retro_pabe_1218, retro_pabe_1452, retro_pabe_1717, retro_pabe_1771, retro_pabe_2549, retro_pabe_2557, retro_pabe_2740, retro_pabe_299, retro_pabe_3667, retro_pabe_400, retro_pabe_414, retro_pabe_470, retro_pabe_720, retro_pabe_838,
Pan troglodytes	ENSPTRG00000021436	16 retrocopies	retro_ptro_1232, retro_ptro_1836, retro_ptro_1838, retro_ptro_2073, retro_ptro_2085, retro_ptro_209, retro_ptro_2151, retro_ptro_2152, retro_ptro_225, retro_ptro_2283, retro_ptro_2965, retro_ptro_3140, retro_ptro_321, retro_ptro_561, retro_ptro_913, retro_ptro_953,
Pteropus vampyrus	ENSPVAG00000003437	2 retrocopies	retro_pvam_1198 , retro_pvam_886,
Ictidomys tridecemlineatus	ENSSTOG00000010546	6 retrocopies	retro_itri_1204, retro_itri_1588, retro_itri_477, retro_itri_529, retro_itri_603, retro_itri_876,
Tursiops truncatus	ENSTTRG00000011605	7 retrocopies	retro_ttru_1433, retro_ttru_1600, retro_ttru_181, retro_ttru_1901, retro_ttru_537, retro_ttru_919, retro_ttru_931,

	RetrogeneDB ID:	retro_pvam_1198
Retrocopy location	Organism:	*Megabat (Pteropus vampyrus)*
	Coordinates:	scaffold_40318:1072..1757(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	SET
	Ensembl ID:	ENSPVAG00000003437
	Aliases:	None
	Description:	SET nuclear oncogene [Source:HGNC Symbol;Acc:10760]

Parental	EIDRLNEQASEEILKVEQKYNKLRQPFFQKRSELIAKIPNFWVTTFVNHPQVSALLGEEDEEALHYLTRV
	E.....E.ASEEIL..EQK.NKL...FF.KRSELIA.I........VNH.Q.SALL.EED.E.LH..T.V
Retrocopy	EVRQTKE*ASEEILEAEQKRNKLPTIFF-KRSELIAQIQ--FCCNSVNHHQGSALLREEDDEGLHCMTKV

Parental	EVTEFEDIKSGYRIDFYFDENPYFENKVLSKEFHLNESGDPSSKSTEIKWKSGKDLTKRSSQTQNKASRK
	..TEF.D.K..Y..DFYFDE.PYFE..V.S.EFHL.ESGD.SSKSTEIKWKS.KD..KRSS.T.NKA.R.
Retrocopy	DTTEFDVKIIYKVDFYFDEKPYFESHVSSSEFHLIESGDSSSKSTEIKWKSKKDSMKRSSPTNKANRR

Parental	RQHEEPESF-FTWFTDHSDAGADELGEVIKDDIWPNPLQYYLVPDMDDEEGEGEEDDDDDEEEEGLEDID
	R..EEP.....TW.TDHSD..ADELG.V.KDDIWP..L.Y.LVPDM.DE...GEE..D...EE..LE.ID
Retrocopy	RHYEEPGTY<LTWLTDHSDTCADELGKVLKDDIWPSLLRYHLVPDMYDE---GEEEGDNMVEER-LEVID

Parental	EEGDEDEGEEDEDDDE-GEEGEEDEGED
	EE.DEDE.E..EDDDE.G.EG......D
Retrocopy	EEADEDESELGEDDDE<GGEG*KRNTDD

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

RetrogeneDB ID:

retro_pvam_1198