RetrogeneDB - Retrocopy retro_meug

                        
>retro_meug_1176
GCCCACAAGAAACAGTCAACCATCTTCCAAAACAGTAAGTGAGTGCCTCTTGGGGACACAGCCAAAGACAAGCTGCCCAC

ATACAACAAGAACATTGGGCTGGGCTTCAAGACCCCCAAAGAGGCCATCAAGGGCACCCATGTTGACAAGAAGTCCCCCT

TCACCATCAATATCTCCATCAGAGTCAGCATCCTGTCTGGTGCGGTGACCAAGATAAAGATGCAAAGAACATCATCATCC

ACCAGGACTACCTACATCAGATCCTCAAATACAACTGATTGGAGAAACACCACAAGAACGTGTCTGCATACCTGTCACCC

TGCTTCTGGGATGTCCATGTTGGAGACATTGTGACCATGAGTGAGTGCAGGCCCCTCAGCACAGCCGTGAGGTTCAATGT

ACTGAAGGTCATCAAGGCAGCCAGAACCCAAAAGCAATTCCAA

ORF - retro_meug_1176 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	72.48 %
Parental protein coverage:	96.73 %
Number of stop codons detected:	2
Number of frameshifts detected:	1

Retrocopy - Parental Gene Alignment:

                                ParentalAYQKQPTIFQNKKRVLLGDTAKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPFTGNVSIRGRILSGVVT
A..KQ.TIFQN.K.V.LGDTAK.KLP.Y.KNIGLGFKTPKEAI.GT..DKK.PFT.N.SIR..ILSG.VT
RetrocopyAHKKQSTIFQNSK*VPLGDTAKDKLPTYNKNIGLGFKTPKEAIKGTHVDKKSPFTINISIRVSILSGAVT
ParentalKMKMQRT-IVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGECRPLSKTVRFNVLKVTK
K.KMQRT.I.I..DYLH.I.KYN..EK.HKN.S..LSPCF.DV..GDIVT..ECRPLS..VRFNVLKV.K
RetrocopyKIKMQRT<IIIHQDYLHQILKYN*LEKHHKNVSAYLSPCFWDVHVGDIVTMSECRPLSTAVRFNVLKVIK
ParentalAAGTKKQFQ
AA.T.KQFQ
RetrocopyAARTQKQFQ

                            

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

                        

RNA-Seq - click to see more details

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Macropus eugenii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_meug_1176 retrocopy.

TSS - click to see more details

Macropus eugenii was not studied using FANTOM5 data.

Lab - click to see more details

retro_meug_1176 was not experimentally validated.

Retrocopy orthology:

Macropus eugenii 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 17 parental genes, and 100 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014020	13 retrocopies	retro_amel_1038, retro_amel_1071, retro_amel_1398, retro_amel_1406, retro_amel_1475, retro_amel_246, retro_amel_262, retro_amel_317, retro_amel_64, retro_amel_757, retro_amel_759, retro_amel_764, retro_amel_859,
Bos taurus	ENSBTAG00000013924	5 retrocopies	retro_btau_1282, retro_btau_1369, retro_btau_1499, retro_btau_1529, retro_btau_888,
Canis familiaris	ENSCAFG00000003631	9 retrocopies	retro_cfam_126, retro_cfam_1333, retro_cfam_1572, retro_cfam_1656, retro_cfam_1669, retro_cfam_1900, retro_cfam_1955, retro_cfam_2121, retro_cfam_248,
Callithrix jacchus	ENSCJAG00000000069	1 retrocopy	retro_cjac_340,
Danio rerio	ENSDARG00000053058	1 retrocopy	retro_drer_15,
Equus caballus	ENSECAG00000000370	1 retrocopy	retro_ecab_868,
Felis catus	ENSFCAG00000009196	13 retrocopies	retro_fcat_1362, retro_fcat_1491, retro_fcat_1535, retro_fcat_1564, retro_fcat_1719, retro_fcat_1945, retro_fcat_197, retro_fcat_1991, retro_fcat_273, retro_fcat_507, retro_fcat_792, retro_fcat_854, retro_fcat_995,
Macropus eugenii	ENSMEUG00000008649	2 retrocopies	retro_meug_1176 , retro_meug_1640,
Monodelphis domestica	ENSMODG00000013434	7 retrocopies	retro_mdom_1185, retro_mdom_1284, retro_mdom_1421, retro_mdom_1950, retro_mdom_636, retro_mdom_922, retro_mdom_978,
Otolemur garnettii	ENSOGAG00000004627	7 retrocopies	retro_ogar_1290, retro_ogar_1813, retro_ogar_1910, retro_ogar_2037, retro_ogar_2573, retro_ogar_2640, retro_ogar_840,
Pelodiscus sinensis	ENSPSIG00000011089	1 retrocopy	retro_psin_35,
Pan troglodytes	ENSPTRG00000011299	1 retrocopy	retro_ptro_88,
Rattus norvegicus	ENSRNOG00000020595	18 retrocopies	retro_rnor_1132, retro_rnor_1159, retro_rnor_1261, retro_rnor_1299, retro_rnor_1363, retro_rnor_1414, retro_rnor_1435, retro_rnor_1451, retro_rnor_1635, retro_rnor_1790, retro_rnor_2000, retro_rnor_2647, retro_rnor_385, retro_rnor_394, retro_rnor_538, retro_rnor_737, retro_rnor_835, retro_rnor_989,
Sorex araneus	ENSSARG00000003236	2 retrocopies	retro_sara_11, retro_sara_469,
Sarcophilus harrisii	ENSSHAG00000004991	1 retrocopy	retro_shar_649,
Ictidomys tridecemlineatus	ENSSTOG00000023443	2 retrocopies	retro_itri_1033, retro_itri_805,
Tupaia belangeri	ENSTBEG00000016677	16 retrocopies	retro_tbel_125, retro_tbel_1361, retro_tbel_1753, retro_tbel_2071, retro_tbel_2207, retro_tbel_2808, retro_tbel_2947, retro_tbel_319, retro_tbel_3401, retro_tbel_3571, retro_tbel_3600, retro_tbel_3742, retro_tbel_449, retro_tbel_604, retro_tbel_801, retro_tbel_836,

	RetrogeneDB ID:	retro_meug_1176
Retrocopy location	Organism:	*Wallaby (Macropus eugenii)*
	Coordinates:	Scaffold31562:10815..11258(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	RPS11
	Ensembl ID:	ENSMEUG00000008649
	Aliases:	None
	Description:	ribosomal protein S11 [Source:HGNC Symbol;Acc:10384]

Parental	AYQKQPTIFQNKKRVLLGDTAKEKLPRYYKNIGLGFKTPKEAIEGTYIDKKCPFTGNVSIRGRILSGVVT
	A..KQ.TIFQN.K.V.LGDTAK.KLP.Y.KNIGLGFKTPKEAI.GT..DKK.PFT.N.SIR..ILSG.VT
Retrocopy	AHKKQSTIFQNSK*VPLGDTAKDKLPTYNKNIGLGFKTPKEAIKGTHVDKKSPFTINISIRVSILSGAVT

Parental	KMKMQRT-IVIRRDYLHYIRKYNRFEKRHKNMSVHLSPCFRDVQIGDIVTVGECRPLSKTVRFNVLKVTK
	K.KMQRT.I.I..DYLH.I.KYN..EK.HKN.S..LSPCF.DV..GDIVT..ECRPLS..VRFNVLKV.K
Retrocopy	KIKMQRT<IIIHQDYLHQILKYN*LEKHHKNVSAYLSPCFWDVHVGDIVTMSECRPLSTAVRFNVLKVIK

Parental	AAGTKKQFQ
	AA.T.KQFQ
Retrocopy	AARTQKQFQ

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

RetrogeneDB ID:

retro_meug_1176