RetrogeneDB - Retrocopy retro_sscr

                        
>retro_sscr_1150
CAAGTGGCCTTCCCTTTCACCCTGGCCGTTGATGATCCCTCAGGGAAGAGCCTTGTGGAAAACCCACATGCTCCCTGGAA

AGATGATACCCTGGTGATCACACACTGTAATCGCACTACAGCAGGAAGAGATCTGTGGCTCTGGGCAGAGGCGCCACAAG

AGGAAAATCTCAGAAACGAAGTGCTCCAGTTCAGCACAAACTGCCTGGAGTACCCTGTTCTGGCCCAGACCGACCTGAAG

CTAGTTGGAATCCCCCGTTTAAGGAGGTTATCATCATGGCTACCAACTGCAAGAATTGTAGCCATTGGACCAATGAGGTG

AAATCTGGAGGAGCCATAGAGCCCTTGGGCACCAGGATCACCCTCCACATCCCAGATCCTGAGATATGAGCAGAGACCTG

CTCCGGTTCAAGACATGTAGCATGGAAATCTTAGAGCAGGAATTTGAACTGGGAATGGCTGTCCTCAGGGGCAGGTTCAT

CACACTGGAGCGGATGCTGAAGCTTGTCTGGGAACTGGTGACCAGGAAACTTTTCACGCTGGGTGACAGTTCCATTCCTG

GCCAGGTGGAGAAACTGCAGGAGTTTAGCCAGAGGTTGGACCAGATCCCTGAGGGTAACATGAAGGCCCACTTTGTTATG

GATGATCCAGCTGGAAACAGCTACTTGCAGAATATACATACACCTGAAGATTATCCTGAGATGAAGGTAGAGCATTATAA

GTGCACATTTGACCCAAACGAGCAGCTAGGGCTCAACGGCATGAAGACGGAGGGCTATGAGACAGGCCTGGCTTCCCAG

ORF - retro_sscr_1150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	69.71 %
Parental protein coverage:	60.18 %
Number of stop codons detected:	0
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalKVYSPFTLVIDDPSGNSFVENPHAPQKDESLEITRYSRTLQQEEMLGLRAGAPEEKPEEEDFRKEVLQFN
.V..PFTL..DDPSG.S.VENPHAP.KD..L.IT...RT......L.L.A.AP.E....E..R.EVLQF.
RetrocopyQVAFPFTLAVDDPSGKSLVENPHAPWKDDTLVITHCNRTTAGRD-LWLWAEAPQE----ENLRNEVLQFS
ParentalTNCPECNAPAQTNMKLVQIPH-FKEVIIMATNCENCGHRTNEVKSGGAIEPLGTRITFHITDPS-DMTRD
TNC.E....AQT..KLV.IP..FKEVIIMATNC.NC.H.TNEVKSGGAIEPLGTRIT.HI.DP..DM.RD
RetrocopyTNCLEYPVLAQTDLKLVGIPR<FKEVIIMATNCKNCSHWTNEVKSGGAIEPLGTRITLHIPDPE<DMSRD
ParentalLLKSETCSVEIPELEFELGMAVLGGKFTTLEGMLNDIRELVTKNPFTLGDSSNPGQAAKLQEFSQKLDQI
LL...TCS.EI.E.EFELGMAVL.G.F.TLE.ML....ELVT...FTLGDSS.PGQ..KLQEFSQ.LDQI
RetrocopyLLRFKTCSMEILEQEFELGMAVLRGRFITLERMLKLVWELVTRKLFTLGDSSIPGQVEKLQEFSQRLDQI
ParentalLEGNMKAHFIMDDPAGNSYLQNVYAPEDDPEMKVEQYKRTFDQNEELGLNDMKTEGYETGLAAQ
.EGNMKAHF.MDDPAGNSYLQN...PED.PEMKVE.YK.TFD.NE.LGLN.MKTEGYETGLA.Q
RetrocopyPEGNMKAHFVMDDPAGNSYLQNIHTPEDYPEMKVEHYKCTFDPNEQLGLNGMKTEGYETGLASQ

                            

                            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	26 .02 RPM
SRP014902_testis	0 .14 RPM	77 .09 RPM
SRP018288_heart	0 .00 RPM	29 .02 RPM
SRP018288_kidney	0 .00 RPM	61 .07 RPM
SRP018288_liver	0 .00 RPM	394 .18 RPM
SRP018288_lung	0 .00 RPM	52 .64 RPM
SRP018856_adipose	0 .23 RPM	51 .30 RPM
SRP035408_brain	0 .00 RPM	83 .82 RPM
SRP035408_liver	0 .00 RPM	134 .24 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_1150 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_1150 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_sscr_1150 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000011907	1 retrocopy	retro_etel_246,
Homo sapiens	ENSG00000109917	1 retrocopy	retro_hsap_3639,
Gorilla gorilla	ENSGGOG00000000664	1 retrocopy	retro_ggor_2455,
Myotis lucifugus	ENSMLUG00000014012	1 retrocopy	retro_mluc_2167,
Macaca mulatta	ENSMMUG00000020287	1 retrocopy	retro_mmul_1808,
Mus musculus	ENSMUSG00000032078	2 retrocopies	retro_mmus_3602, retro_mmus_3701,
Otolemur garnettii	ENSOGAG00000009977	1 retrocopy	retro_ogar_506,
Pongo abelii	ENSPPYG00000025914	1 retrocopy	retro_pabe_2986,
Pan troglodytes	ENSPTRG00000004312	1 retrocopy	retro_ptro_2464,
Sus scrofa	ENSSSCG00000015066	1 retrocopy	retro_sscr_1150 ,

	RetrogeneDB ID:	retro_sscr_1150
Retrocopy location	Organism:	*Pig (Sus scrofa)*
	Coordinates:	X:36762595..36763394(+)
	Located in intron of:	ENSSSCG00000027777
Retrocopy information	Ensembl ID:	ENSSSCG00000030880
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	ZNF259
	Ensembl ID:	ENSSSCG00000015066
	Aliases:	None
	Description:	zinc finger protein 259 [Source:HGNC Symbol;Acc:13051]

Parental	KVYSPFTLVIDDPSGNSFVENPHAPQKDESLEITRYSRTLQQEEMLGLRAGAPEEKPEEEDFRKEVLQFN
	.V..PFTL..DDPSG.S.VENPHAP.KD..L.IT...RT......L.L.A.AP.E....E..R.EVLQF.
Retrocopy	QVAFPFTLAVDDPSGKSLVENPHAPWKDDTLVITHCNRTTAGRD-LWLWAEAPQE----ENLRNEVLQFS

Parental	TNCPECNAPAQTNMKLVQIPH-FKEVIIMATNCENCGHRTNEVKSGGAIEPLGTRITFHITDPS-DMTRD
	TNC.E....AQT..KLV.IP..FKEVIIMATNC.NC.H.TNEVKSGGAIEPLGTRIT.HI.DP..DM.RD
Retrocopy	TNCLEYPVLAQTDLKLVGIPR<FKEVIIMATNCKNCSHWTNEVKSGGAIEPLGTRITLHIPDPE<DMSRD

Parental	LLKSETCSVEIPELEFELGMAVLGGKFTTLEGMLNDIRELVTKNPFTLGDSSNPGQAAKLQEFSQKLDQI
	LL...TCS.EI.E.EFELGMAVL.G.F.TLE.ML....ELVT...FTLGDSS.PGQ..KLQEFSQ.LDQI
Retrocopy	LLRFKTCSMEILEQEFELGMAVLRGRFITLERMLKLVWELVTRKLFTLGDSSIPGQVEKLQEFSQRLDQI

Parental	LEGNMKAHFIMDDPAGNSYLQNVYAPEDDPEMKVEQYKRTFDQNEELGLNDMKTEGYETGLAAQ
	.EGNMKAHF.MDDPAGNSYLQN...PED.PEMKVE.YK.TFD.NE.LGLN.MKTEGYETGLA.Q
Retrocopy	PEGNMKAHFVMDDPAGNSYLQNIHTPEDYPEMKVEHYKCTFDPNEQLGLNGMKTEGYETGLASQ

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

RetrogeneDB ID:

retro_sscr_1150