RetrogeneDB - Retrocopy retro_sscr

                        
>retro_sscr_59
ATGGCAGCTCCGAAGACCACAGGTGTGGGGCCGTTGGTGGGAGCAGTGGTCCAGGGTACTAACTCCACTCATTTTATGGT

TTTCAATTCAAAAACAGCAGAACTCCTTAGTCACCATCAGGTGGAATTAACACAAGTGTTCCCAAAAGAAGGATGGGTGG

AACAAGACCCCAAGCTCATTCTTCAGTCTGTGTATGAATGTATAGAGAGAACATGCGAGAAACTTGAAGAACTGCACGTT

GACCTCTCCAACATAAAAGCCGTGGGCGTCAGCAATCAGAGGGAAACCACGGTCGTCTGGGACAGGCTCACGGGGGAGCC

GCTCTACAACGCCGTGGTGTGGCTCGACCTGAGAACCCAGTCCACCGTGGAGCTCCTCAGCAAAAAAATTCCAGGGAATA

ATAACTTCGTCAAGTCCAAGACAGGCCTGCCCCTCAGCACTTACTTCAGTGCGGTGAAGCTTCGCTGGCTTCTTGACAAC

GTGAGTCAAGTTCAGAAGGCGGTTCGAGAAGGCAGAGCTCTTTTTGGTACCATCGATTCCTGGCTTATCTGGAGCATGAC

TGGAGGGGCTCACGGAGGCATCCACTGCACAGATGTAACAAATGCAAGCAGGACGATGCTCTTCAACATCCACTCTCTGC

AATGGGACAAAGAGCTGTGCGATTTCTTTGAAATTCCAATGGGCATTCTTCCAGACGTCTGGAGCTCTTCGGAGATCTAT

GGCCTAATGAAAACCGGGGCCTTGGAAGGCGTGCCCATATCAGGGTGCTTGGGGGACCAGTCTGCTGCATTAGTAGGACA

AATGTGCTTCCAGGAAGGACAAGCCAAAAACACATATGGAACAGGCTGTTTCTTACTATGTAATACAGGCCACAAGTGTG

TATTTTCGGAGCATGGCCTGCTGACCACGGTGGCTTACAAACTAGGCAAAGACCAGCCAGTATGTTATGCGCTAGAAGGT

TCTGTCGCTATAGCTGGTGCTGTTATTCGCTGGCTACGAGACAACCTTGGAATTATAAAGACCTCCGAAGAAAGTGAAAA

ACTTGCTAAAGAAGTAGGTACTTCTTACGGCTGCTACTTCATCCCAGCCTTTTCAGGATTATACGCACCTTATTGGGAGC

CCACGGCAAGAGGGATAATCTGTGGTCTCACTCAGTTCACCAATAAAAGTCATATTGCTTTCGCTGCATTAGAAGCTATT

TGTTTCCAAACCCGAGAGATTTTGGATGCCATGAACCGTGACTGTGGAATTCCACTTAATCATCTGCAAGTAGATGGAGG

AATGACCACCAACAAAGTCCTTATGCAACTGCAAGCAGACATTCTGCATATTCCAGTAATAAGAGCCTCTATGCCCGAAA

CGACTGCACTGGGAGCTGCCATGGCAGCAGGAGCCGCACATGGGGTGGACGTCTGGAGTCTTAAACCTGAGGATCTGTCA

ACTGTCATGATGGAACGGTTTGAACCACAGATCAAGGCCACAGAAAGTGAAATTCGTTACTCTACATGGAAGAAAGCTGT

GATGAAGTCAATGGGTTGGGTTACAACTCAGCCTCCTGAAAGTAGTGAACCTACCCTGTTCTCTAGTCTGCCCTTGGGTT

TTTTTATAGTTAGCAGCATGATACTGTTAATTGGAGCAAGATACATCTCCGGTATACCATAA

ORF - retro_sscr_59 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	86.45 %
Parental protein coverage:	100.0 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalMAAANKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVELKQEFPKEGWVEQDPKEILNSVYECIEK
MAA......GPLVGAV.QGT.ST.F.VFNSKTAELLSHHQVEL.Q.FPKEGWVEQDPK.IL.SVYECIE.
RetrocopyMAAPKTTGVGPLVGAVVQGTNSTHFMVFNSKTAELLSHHQVELTQVFPKEGWVEQDPKLILQSVYECIER
ParentalTCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK
TCEKL..L..D.SNIKA.GVSNQRETTVVWD.LTGEPLYNAVVWLDLRTQSTVE.LSK.IPGNNNFVKSK
RetrocopyTCEKLEELHVDLSNIKAVGVSNQRETTVVWDRLTGEPLYNAVVWLDLRTQSTVELLSKKIPGNNNFVKSK
ParentalTGLPLSTYFSAVKLRWLLDNVRKVQKAVEEERALFGTVDSWLIWCLTGGANGGVHCTDVTNASRTMLFNI
TGLPLSTYFSAVKLRWLLDNV..VQKAV.E.RALFGT.DSWLIW..TGGA.GG.HCTDVTNASRTMLFNI
RetrocopyTGLPLSTYFSAVKLRWLLDNVSQVQKAVREGRALFGTIDSWLIWSMTGGAHGGIHCTDVTNASRTMLFNI
ParentalHSLEWDKELCEFFEIPMKILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
HSL.WDKELC.FFEIPM.ILP.V.SSSEIYGLMK.GALEGVPISGCLGDQSAALVGQMCFQ.GQAKNTYG
RetrocopyHSLQWDKELCDFFEIPMGILPDVWSSSEIYGLMKTGALEGVPISGCLGDQSAALVGQMCFQEGQAKNTYG
ParentalTGCFLLCNTGRKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVVRWLRDNLGIIKTSEEIEKLAK
TGCFLLCNTG.KCVFSEHGLLTTVAYKLG.D.PV.YALEGSVAIAGAV.RWLRDNLGIIKTSEE.EKLAK
RetrocopyTGCFLLCNTGHKCVFSEHGLLTTVAYKLGKDQPVCYALEGSVAIAGAVIRWLRDNLGIIKTSEESEKLAK
ParentalEVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNRCHIAFAALEAVCFQTREILDAMNRDCGMPLR
EVGTSYGCYF.PAFSGLYAPYWEP.ARGIICGLTQFTN..HIAFAALEA.CFQTREILDAMNRDCG.PL.
RetrocopyEVGTSYGCYFIPAFSGLYAPYWEPTARGIICGLTQFTNKSHIAFAALEAICFQTREILDAMNRDCGIPLN
ParentalHLQVDGGMTNNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLDPEDLSAVTVERFEPQ
HLQVDGGMT.NK.LMQLQADIL.IPV...SMPETTALGAAMAAGAA.GV.VWSL.PEDLS.V..ERFEPQ
RetrocopyHLQVDGGMTTNKVLMQLQADILHIPVIRASMPETTALGAAMAAGAAHGVDVWSLKPEDLSTVMMERFEPQ
ParentalINAEESEIRYSTWKKAVMKSMGWVTTQSSESGMP
I.A.ESEIRYSTWKKAVMKSMGWVTTQ..ES..P
RetrocopyIKATESEIRYSTWKKAVMKSMGWVTTQPPESSEP

                            

                            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	4 .25 RPM
SRP014902_testis	0 .28 RPM	2 .55 RPM
SRP018288_heart	0 .00 RPM	30 .04 RPM
SRP018288_kidney	0 .00 RPM	184 .80 RPM
SRP018288_liver	0 .00 RPM	110 .82 RPM
SRP018288_lung	0 .00 RPM	20 .67 RPM
SRP018856_adipose	0 .00 RPM	22 .26 RPM
SRP035408_brain	0 .00 RPM	4 .83 RPM
SRP035408_liver	0 .00 RPM	94 .14 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

21 EST(s) were mapped to retro_sscr_59 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CV864867	147411080	147411633	99.9	552	1	551
CV866485	147410521	147411009	99.8	487	1	486
CV866995	147410955	147411401	100	446	0	446
CV867146	147410494	147411009	99.7	513	2	511
CV867277	147410545	147411088	99.9	542	1	541
CV868803	147410396	147411009	99.7	611	2	609
CV870340	147410506	147411137	99.6	628	3	625
CV870707	147410518	147411156	99.6	634	3	630
CV872092	147410518	147411157	99.6	636	3	633
CV872556	147410721	147411402	99.9	680	1	679
CV875200	147410502	147411192	99.8	688	2	686
CV876778	147410535	147411115	99.9	579	1	578
CV877158	147410518	147411103	99.7	583	2	581
CV878276	147410804	147411469	100	665	0	665
CX057597	147410518	147411137	99.6	616	3	613
CX058802	147410502	147411089	99.4	582	4	577
CX061095	147410935	147411512	100	576	0	575
CX062853	147410489	147411161	99.5	668	4	664
CX063416	147410806	147411425	99.7	617	2	615
CX063736	147410506	147411113	99.9	606	1	605
EW033951	147411544	147411748	100	204	0	204

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_59 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_sscr_59 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_70
Callithrix jacchus	retro_cjac_125
Mus musculus	retro_mmus_119
Rattus norvegicus	retro_rnor_34
Canis familiaris	retro_cfam_19

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003261	2 retrocopies	retro_cpor_11, retro_cpor_20,
Felis catus	ENSFCAG00000004264	1 retrocopy	retro_fcat_140,
Monodelphis domestica	ENSMODG00000002417	1 retrocopy	retro_mdom_234,
Oryctolagus cuniculus	ENSOCUG00000013023	2 retrocopies	retro_ocun_2, retro_ocun_81,
Pteropus vampyrus	ENSPVAG00000012460	1 retrocopy	retro_pvam_1417,
Sarcophilus harrisii	ENSSHAG00000006470	1 retrocopy	retro_shar_35,
Sus scrofa	ENSSSCG00000012202	2 retrocopies	retro_sscr_479, retro_sscr_59 ,

	RetrogeneDB ID:	retro_sscr_59
Retrocopy location	Organism:	*Pig (Sus scrofa)*
	Coordinates:	8:147410516..147412178(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSSSCG00000009257
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	GK
	Ensembl ID:	ENSSSCG00000012202
	Aliases:	None
	Description:	glycerol kinase [Source:HGNC Symbol;Acc:4289]

Parental	MAAANKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVELKQEFPKEGWVEQDPKEILNSVYECIEK
	MAA......GPLVGAV.QGT.ST.F.VFNSKTAELLSHHQVEL.Q.FPKEGWVEQDPK.IL.SVYECIE.
Retrocopy	MAAPKTTGVGPLVGAVVQGTNSTHFMVFNSKTAELLSHHQVELTQVFPKEGWVEQDPKLILQSVYECIER

Parental	TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK
	TCEKL..L..D.SNIKA.GVSNQRETTVVWD.LTGEPLYNAVVWLDLRTQSTVE.LSK.IPGNNNFVKSK
Retrocopy	TCEKLEELHVDLSNIKAVGVSNQRETTVVWDRLTGEPLYNAVVWLDLRTQSTVELLSKKIPGNNNFVKSK

Parental	TGLPLSTYFSAVKLRWLLDNVRKVQKAVEEERALFGTVDSWLIWCLTGGANGGVHCTDVTNASRTMLFNI
	TGLPLSTYFSAVKLRWLLDNV..VQKAV.E.RALFGT.DSWLIW..TGGA.GG.HCTDVTNASRTMLFNI
Retrocopy	TGLPLSTYFSAVKLRWLLDNVSQVQKAVREGRALFGTIDSWLIWSMTGGAHGGIHCTDVTNASRTMLFNI

Parental	HSLEWDKELCEFFEIPMKILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
	HSL.WDKELC.FFEIPM.ILP.V.SSSEIYGLMK.GALEGVPISGCLGDQSAALVGQMCFQ.GQAKNTYG
Retrocopy	HSLQWDKELCDFFEIPMGILPDVWSSSEIYGLMKTGALEGVPISGCLGDQSAALVGQMCFQEGQAKNTYG

Parental	TGCFLLCNTGRKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVVRWLRDNLGIIKTSEEIEKLAK
	TGCFLLCNTG.KCVFSEHGLLTTVAYKLG.D.PV.YALEGSVAIAGAV.RWLRDNLGIIKTSEE.EKLAK
Retrocopy	TGCFLLCNTGHKCVFSEHGLLTTVAYKLGKDQPVCYALEGSVAIAGAVIRWLRDNLGIIKTSEESEKLAK

Parental	EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNRCHIAFAALEAVCFQTREILDAMNRDCGMPLR
	EVGTSYGCYF.PAFSGLYAPYWEP.ARGIICGLTQFTN..HIAFAALEA.CFQTREILDAMNRDCG.PL.
Retrocopy	EVGTSYGCYFIPAFSGLYAPYWEPTARGIICGLTQFTNKSHIAFAALEAICFQTREILDAMNRDCGIPLN

Parental	HLQVDGGMTNNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLDPEDLSAVTVERFEPQ
	HLQVDGGMT.NK.LMQLQADIL.IPV...SMPETTALGAAMAAGAA.GV.VWSL.PEDLS.V..ERFEPQ
Retrocopy	HLQVDGGMTTNKVLMQLQADILHIPVIRASMPETTALGAAMAAGAAHGVDVWSLKPEDLSTVMMERFEPQ

Parental	INAEESEIRYSTWKKAVMKSMGWVTTQSSESGMP
	I.A.ESEIRYSTWKKAVMKSMGWVTTQ..ES..P
Retrocopy	IKATESEIRYSTWKKAVMKSMGWVTTQPPESSEP

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

RetrogeneDB ID:

retro_sscr_59