RetrogeneDB - Retrocopy retro_sscr

                        
>retro_sscr_1102
AGGCAAGGGATCTGGCAAAGAAATACTGGCCAAAAACTCAAAGGAAGCTGCCTTGGAATCATCGATGGAAGAAATATTTA

AAATTGATCAGATAGGATCAATTACTGCTTGAGGGGCTGCTGCTAGTCTTGGAGCATTGCACTACAATAGCTTTGGAATG

TCTATTGGGATTGGAGCTATGGAAAAGGCTGTAATTTGGCCTCAGCATGTGAAGGATAGAGTTCATTCTACCCACGTGTC

CTTAGCAGGAAGTACCGGTTTAACAGCTTTGTCTGCCCTAGCAATGAGCAGAACTCTGCTTCTCATGAACTTCATGATAA

CAAGTTCTTGAGTGATAATTGGTACCTTTGCAGACATGATTGGAGCTGGAATCCTGGTACAATTGGCACTGTGGAACTGG

AGCCCAGGCCCAAAGCATCTCGCCTGGTTACTACATGCTTGTGTGGTGGGAGCAATGGTGACTCCTCTAACAATATTAGG

GGAGCCTCTTCTCATCAGAGTTGGGTGGTACACAGCAGCCACTGTGGGACGTCTCTCCACTGTTGCCATGTATGCACCTC

TGAGAAGTGTGGAACATGGGAGTACCCTGGGGGCAGTGGGCTGGGTGGGTCTTTGTACCGAGT

ORF - retro_sscr_1102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	65.73 %
Parental protein coverage:	60.87 %
Number of stop codons detected:	2
Number of frameshifts detected:	3

Retrocopy - Parental Gene Alignment:

                                ParentalRIGIRRGKTGQELK-EAALEPSVEKIFKIDQMGRWFIAGGAAVGLGALCYYGLGMSNEIGAIEKAIIWPQ
R.GI....TGQ.LK.EAALE.S.E.IFKIDQ.G....A.GAA..LGAL.Y...GMS..IGA.EKA.IWPQ
RetrocopyRQGIWQRNTGQKLK>EAALESSMEEIFKIDQIGS-ITA*GAAASLGALHYNSFGMSIGIGAMEKAVIWPQ
ParentalYVKDRIHSTYMYLAGSIGLTAMSALAVSRTPALMNFMMKGSWVTIGATFAAMIGAGMLVQSISYDRSPGP
.VKDR.HST...LAGS.GLTA.SALA.SRT..LMNFM...S.V.IG.TFA.MIGAG.LVQ......SPGP
RetrocopyHVKDRVHSTHVSLAGSTGLTALSALAMSRTLLLMNFMITSS*VIIG-TFADMIGAGILVQLALWNWSPGP
ParentalKHLAWLLHSGVMGAVVAPLTILGGPLLIRAAWYTAGIVGGLSTVAMCAP-SEK-FLNMGAPLGVGLGLVF
KHLAWLLH..V.GA.V.PLTILG.PLLIR..WYTA..VG.LSTVAM.AP.SEK...NMG.P.G...G.VF
RetrocopyKHLAWLLHACVVGAMVTPLTILGEPLLIRVGWYTAATVGRLSTVAMYAP<SEK<VWNMGVPWGQWAGWVF
ParentalVSS
V.S
RetrocopyVPS

                            

                            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
SRP014902_placenta	0 .00 RPM	69 .29 RPM
SRP014902_testis	0 .14 RPM	61 .67 RPM
SRP018288_heart	0 .00 RPM	255 .13 RPM
SRP018288_kidney	0 .00 RPM	490 .36 RPM
SRP018288_liver	0 .00 RPM	258 .57 RPM
SRP018288_lung	0 .00 RPM	43 .28 RPM
SRP018856_adipose	0 .00 RPM	148 .21 RPM
SRP035408_brain	0 .00 RPM	137 .14 RPM
SRP035408_liver	0 .00 RPM	156 .08 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_sscr_1102 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_1102 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_sscr_1102 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009753	1 retrocopy	retro_amel_336,
Bos taurus	ENSBTAG00000032829	2 retrocopies	retro_btau_1689, retro_btau_779,
Choloepus hoffmanni	ENSCHOG00000001576	1 retrocopy	retro_chof_5,
Cavia porcellus	ENSCPOG00000006432	1 retrocopy	retro_cpor_1436,
Dasypus novemcinctus	ENSDNOG00000018880	5 retrocopies	retro_dnov_2426, retro_dnov_2514, retro_dnov_2524, retro_dnov_708, retro_dnov_812,
Dipodomys ordii	ENSDORG00000001109	1 retrocopy	retro_dord_184,
Echinops telfairi	ENSETEG00000001796	1 retrocopy	retro_etel_68,
Loxodonta africana	ENSLAFG00000009646	1 retrocopy	retro_lafr_388,
Macropus eugenii	ENSMEUG00000009861	3 retrocopies	retro_meug_1431, retro_meug_1806, retro_meug_798,
Microcebus murinus	ENSMICG00000011621	1 retrocopy	retro_mmur_692,
Monodelphis domestica	ENSMODG00000001693	3 retrocopies	retro_mdom_1008, retro_mdom_407, retro_mdom_886,
Oryctolagus cuniculus	ENSOCUG00000006093	1 retrocopy	retro_ocun_260,
Otolemur garnettii	ENSOGAG00000012120	1 retrocopy	retro_ogar_1287,
Rattus norvegicus	ENSRNOG00000013961	1 retrocopy	retro_rnor_2461,
Sus scrofa	ENSSSCG00000010345	1 retrocopy	retro_sscr_1102 ,
Tupaia belangeri	ENSTBEG00000016365	2 retrocopies	retro_tbel_1601, retro_tbel_2819,
Tarsius syrichta	ENSTSYG00000006367	1 retrocopy	retro_tsyr_4,
Drosophila melanogaster	FBgn0030263	1 retrocopy	retro_dmel_61,

	RetrogeneDB ID:	retro_sscr_1102
Retrocopy location	Organism:	*Pig (Sus scrofa)*
	Coordinates:	GL894649.2:5830..6453(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	GHITM
	Ensembl ID:	ENSSSCG00000010345
	Aliases:	None
	Description:	growth hormone inducible transmembrane protein [Source:HGNC Symbol;Acc:17281]

Parental	RIGIRRGKTGQELK-EAALEPSVEKIFKIDQMGRWFIAGGAAVGLGALCYYGLGMSNEIGAIEKAIIWPQ
	R.GI....TGQ.LK.EAALE.S.E.IFKIDQ.G....A.GAA..LGAL.Y...GMS..IGA.EKA.IWPQ
Retrocopy	RQGIWQRNTGQKLK>EAALESSMEEIFKIDQIGS-ITA*GAAASLGALHYNSFGMSIGIGAMEKAVIWPQ

Parental	YVKDRIHSTYMYLAGSIGLTAMSALAVSRTPALMNFMMKGSWVTIGATFAAMIGAGMLVQSISYDRSPGP
	.VKDR.HST...LAGS.GLTA.SALA.SRT..LMNFM...S.V.IG.TFA.MIGAG.LVQ......SPGP
Retrocopy	HVKDRVHSTHVSLAGSTGLTALSALAMSRTLLLMNFMITSS*VIIG-TFADMIGAGILVQLALWNWSPGP

Parental	KHLAWLLHSGVMGAVVAPLTILGGPLLIRAAWYTAGIVGGLSTVAMCAP-SEK-FLNMGAPLGVGLGLVF
	KHLAWLLH..V.GA.V.PLTILG.PLLIR..WYTA..VG.LSTVAM.AP.SEK...NMG.P.G...G.VF
Retrocopy	KHLAWLLHACVVGAMVTPLTILGEPLLIRVGWYTAATVGRLSTVAMYAP<SEK<VWNMGVPWGQWAGWVF

Parental	VSS
	V.S
Retrocopy	VPS

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

RetrogeneDB ID:

retro_sscr_1102