RetrogeneDB - Retrocopy retro_nleu

                        
>retro_nleu_2157
GTTTCTGAAACACAGAATATAGAATCCCAGAAGATTCACTCCTCTAGACCGAGTGATATAACTAGCTCTAATATGCAAAT

ATGTGGATTTAAAAGCACAGTTCCTCATTTAACCAAAGAAGAAAAGTATCAAAACTTCTCAGTGAAAATAAAATTATAGA

TGAACAGCCTAAACATCAGTCAGATATGTGTGGTCAGAACTTTAACACAAATTTGTTTCAGTTAGGCCATAAATGTGCAG

CTATGTTGGATTTGGTTTGTAGTACTGAACAAATTAATATAGGACCTGAAGTGGTACAAAGAGAGTGTGTGCCAACGGAA

TATCATGAAATACAAAACCAGTGTTTGGGATTATTTTCCTCGAACGCAGTAGATAAGTCAAGGTCCGAAGCAGCAGTTAG

GAAGGTCTCAGACCTTAAAATATCAACTGATACAGAATTTCTCAGTATAATTACCTCCAGCTAGGTTGCTGTTTTAGCTC

AAAAGAAAGATAAAAGGCGGAGTCCTATAAATAAAGGGAATGTAAACATGGAGACTGAACCAAAGGCAAGTTACGGGGAG

GTAAGAATACCTGAAGAGTATTGGATTCAGCTTGATGGTTTTACAGAAACATATGAAAGTGGACAAAACCAAGCATATTC

CCTTGAACTTTTTAGTCCTGTTTGTCCTAAAACAGAAAATAGCCGCATTCACATAAACTCTGATAAAGGTCTTGAAGAAC

ATACGGGATCTCAAGAACTTTTCAGTTCTGAAGATGAACTGCCACCAAATGAGATACGTATTGAGTTGTGTAGCTCAGGA

ATACTGGGTTCCCAACTAAATGCCTTCCACAAAAGTGCTATTAAAAGAAGCTGCACCTCTGAAGATAAAGTGGGCCAGTC

TGAAGCTCTATCTAGAGTCCTTCAAGTAGCTAAGAAAATGAAGTTGATTTCTAATGGAGGAGATTCTGCTGTAGAAATGG

ATCGGAGGAATGTGTCTGAATTTAAGGGTATTAAAAAAATATCATTAATAAAAAAACTGTGATTCTAAAAGCCAGAAGTA

TAATTGTTTACTCATGGTGCTATCTCCATGCCATGTGAAGGAAATAAACATAAAATTCAGGCCAAATTCTGGCTCTAAAG

TGCCTTTAGCAACAGTTACAGTAATTGATCAATCAAAAACTAAGAAGAAGGTTTTTCTGCGGAGGACTGCAGCATTTTGG

GCATTTACAGTGTTTCTTGGAGATATAATTTTACTCACAGATGTTGTATTCATGAGGACCAATGGGTTGGCAAGACAGTA

CTACAATCAACATTTAGCAGTCAGTTATTAAATCTTGGGAGTTATTCATCTATTCAGCCTGAAGAATATTCCAGTATAGT

TAGTGACGTTGTACTTCAAGACTTTCTGGCATATATGTCCTCAAAACATTCCTACCTCAGAGATCTTCCTCCGAGGCAGC

CTCAGAGGGTGAACAGTATCGACTTTGTAGAATTGGAGCACCTTCAACCTGATGTATTAGTCCATGCAGTACTAAGAGTT

GTTGATTTCACTATACTGACAGAGGCAGTATACAGTTATAGAGGACAGAAGCAGAAAAAAGTTATGTTAACAGTGGAACA

GGCCCAAGATCAACATTATGTGCTTGTATTATGGGGTCCTGGAGCAGCCTGGTACCCTCAACTTCAAAGGAAAAAAGGTT

ATATTTGGGAATTTAAATATCTTTTTGTTCAGCACACTTACACACTAGAAAACCTAGAATTGCATACGGTGCCTTGGTCA

TCCTGTGAGTGCTTGTTTGATGATGATATAACGGCAATTACATTTAAAGCAAAATTTCAAAAAAATGCACCCTCCTTTGT

GAAGATATCAGACTTAGCAACCCGCCTAGAGGATAAATGTTCAGGAGTCGTTCTAATTAAAGCCCAGATTTCAGAGCTGG

CATTTCCTATTACAGCAGCTCAGAAGATAGCTCTAAATGCTCACAGTTCTCTGAAGAGTATTTTTTCTTCTCTTCCCAAC

ATCGTATATACTGGCTATGCAAAATGTGGATTGGAACTAGAAACAGATGAGAACAGGATCTACAAA

ORF - retro_nleu_2157 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	93.64 %
Parental protein coverage:	76.22 %
Number of stop codons detected:	1
Number of frameshifts detected:	3

Retrocopy - Parental Gene Alignment:

                                ParentalVSETQNIESQKIHSSRLSDITSSNMQICGFKSTVPHLAKEEKDQ-KLLSENKIIDEQPKHQADICGQNFN
VSETQNIESQKIHSSR.SDITSSNMQICGFKSTVPHL.KEEK.Q.KLLSENKIIDEQPKHQ.D.CGQNFN
RetrocopyVSETQNIESQKIHSSRPSDITSSNMQICGFKSTVPHLTKEEKYQ<KLLSENKIIDEQPKHQSDMCGQNFN
ParentalTDLFQLGHKCAAILDLVCSTEQINIGPEVVQRECVPTEYHEIQNQCLGLFSSNAVDNSRSEAAVRKVSDL
T.LFQLGHKCAA.LDLVCSTEQINIGPEVVQRECVPTEYHEIQNQCLGLFSSNAVD.SRSEAAVRKVSDL
RetrocopyTNLFQLGHKCAAMLDLVCSTEQINIGPEVVQRECVPTEYHEIQNQCLGLFSSNAVDKSRSEAAVRKVSDL
ParentalKISTDTEFLSIITSSQVAFLAQKKDKGRSPINKGNVNMEAEPKASYGEIRIPDENSIQLDGFTEAYESGQ
KISTDTEFLSIITSS.VA.LAQKKDK.RSPINKGNVNME.EPKASYGE.RIP.E..IQLDGFTE.YESGQ
RetrocopyKISTDTEFLSIITSS*VAVLAQKKDKRRSPINKGNVNMETEPKASYGEVRIPEEYWIQLDGFTETYESGQ
ParentalNQAYSLELFSPVCPKTENSCIHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGILCSQLNTFHKS
NQAYSLELFSPVCPKTENS.IHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGIL.SQLN.FHKS
RetrocopyNQAYSLELFSPVCPKTENSRIHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGILGSQLNAFHKS
ParentalAIKRSCTSEDKVGQSEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKGIKKTSLI-KNCDSKSQKYN
AIKRSCTSEDKVGQSEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKGIKK.SLI.KNCDSKSQKYN
RetrocopyAIKRSCTSEDKVGQSEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKGIKKISLI>KNCDSKSQKYN
ParentalCLVMVLSPCHVKEINIKCGRNSGSKVPLATVTVIDESETKKKVFLWRTAAFWAFTVFLGDIILLTDVV-I
CL.MVLSPCHVKEINIK...NSGSKVPLATVTVID.S.TKKKVFL.RTAAFWAFTVFLGDIILLTDVV.I
RetrocopyCLLMVLSPCHVKEINIKFRPNSGSKVPLATVTVIDQSKTKKKVFLRRTAAFWAFTVFLGDIILLTDVV<I
ParentalHEDQWVGETVLQSTFSTQLLNLGSYSSIQPEECSSVVSDVVLQDLLAYVSSKHSYLRDLPPRQPQRVNSI
HEDQWVG.TVLQSTFS.QLLNLGSYSSIQPEE.SS.VSDVVLQD.LAY.SSKHSYLRDLPPRQPQRVNSI
RetrocopyHEDQWVGKTVLQSTFSSQLLNLGSYSSIQPEEYSSIVSDVVLQDFLAYMSSKHSYLRDLPPRQPQRVNSI
ParentalDFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWGPGAAWYPQLQR
DFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWGPGAAWYPQLQR
RetrocopyDFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWGPGAAWYPQLQR
ParentalKKGYIWEFKYLFVQRSYTLENLELHTTPWSSCECLFDDDIRAITFKAKFQKSAPSFVKISDLATHLEDKC
KKGYIWEFKYLFVQ..YTLENLELHT.PWSSCECLFDDDI.AITFKAKFQK.APSFVKISDLAT.LEDKC
RetrocopyKKGYIWEFKYLFVQHTYTLENLELHTVPWSSCECLFDDDITAITFKAKFQKNAPSFVKISDLATRLEDKC
ParentalSGVVLIKAQISELAFPITAAQKIALNAHSSLKSIFSSLPNIVYTGCAKCGLELETDENRIYK
SGVVLIKAQISELAFPITAAQKIALNAHSSLKSIFSSLPNIVYTG.AKCGLELETDENRIYK
RetrocopySGVVLIKAQISELAFPITAAQKIALNAHSSLKSIFSSLPNIVYTGYAKCGLELETDENRIYK

                            

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

                        

RNA-Seq - click to see more details

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Nomascus leucogenys was not studied using ChIP-Seq data.

EST - click to see more details

Nomascus leucogenys was not studied using EST data.

TSS - click to see more details

Nomascus leucogenys was not studied using FANTOM5 data.

Lab - click to see more details

retro_nleu_2157 was not experimentally validated.

Retrocopy orthology:

Nomascus leucogenys 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000017	1 retrocopy	retro_dnov_2237,
Homo sapiens	ENSG00000122376	1 retrocopy	retro_hsap_1370,
Nomascus leucogenys	ENSNLEG00000011652	3 retrocopies	retro_nleu_1073, retro_nleu_2157 , retro_nleu_840,
Pongo abelii	ENSPPYG00000002828	1 retrocopy	retro_pabe_1137,
Pan troglodytes	ENSPTRG00000002465	1 retrocopy	retro_ptro_941,

	RetrogeneDB ID:	retro_nleu_2157
Retrocopy location	Organism:	*Gibbon (Nomascus leucogenys)*
	Coordinates:	GL397332.1:7238958..7241024(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	FAM35A
	Ensembl ID:	ENSNLEG00000011652
	Aliases:	None
	Description:	family with sequence similarity 35, member A [Source:HGNC Symbol;Acc:28773]

Parental	VSETQNIESQKIHSSRLSDITSSNMQICGFKSTVPHLAKEEKDQ-KLLSENKIIDEQPKHQADICGQNFN
	VSETQNIESQKIHSSR.SDITSSNMQICGFKSTVPHL.KEEK.Q.KLLSENKIIDEQPKHQ.D.CGQNFN
Retrocopy	VSETQNIESQKIHSSRPSDITSSNMQICGFKSTVPHLTKEEKYQ<KLLSENKIIDEQPKHQSDMCGQNFN

Parental	TDLFQLGHKCAAILDLVCSTEQINIGPEVVQRECVPTEYHEIQNQCLGLFSSNAVDNSRSEAAVRKVSDL
	T.LFQLGHKCAA.LDLVCSTEQINIGPEVVQRECVPTEYHEIQNQCLGLFSSNAVD.SRSEAAVRKVSDL
Retrocopy	TNLFQLGHKCAAMLDLVCSTEQINIGPEVVQRECVPTEYHEIQNQCLGLFSSNAVDKSRSEAAVRKVSDL

Parental	KISTDTEFLSIITSSQVAFLAQKKDKGRSPINKGNVNMEAEPKASYGEIRIPDENSIQLDGFTEAYESGQ
	KISTDTEFLSIITSS.VA.LAQKKDK.RSPINKGNVNME.EPKASYGE.RIP.E..IQLDGFTE.YESGQ
Retrocopy	KISTDTEFLSIITSS*VAVLAQKKDKRRSPINKGNVNMETEPKASYGEVRIPEEYWIQLDGFTETYESGQ

Parental	NQAYSLELFSPVCPKTENSCIHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGILCSQLNTFHKS
	NQAYSLELFSPVCPKTENS.IHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGIL.SQLN.FHKS
Retrocopy	NQAYSLELFSPVCPKTENSRIHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGILGSQLNAFHKS

Parental	AIKRSCTSEDKVGQSEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKGIKKTSLI-KNCDSKSQKYN
	AIKRSCTSEDKVGQSEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKGIKK.SLI.KNCDSKSQKYN
Retrocopy	AIKRSCTSEDKVGQSEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKGIKKISLI>KNCDSKSQKYN

Parental	CLVMVLSPCHVKEINIKCGRNSGSKVPLATVTVIDESETKKKVFLWRTAAFWAFTVFLGDIILLTDVV-I
	CL.MVLSPCHVKEINIK...NSGSKVPLATVTVID.S.TKKKVFL.RTAAFWAFTVFLGDIILLTDVV.I
Retrocopy	CLLMVLSPCHVKEINIKFRPNSGSKVPLATVTVIDQSKTKKKVFLRRTAAFWAFTVFLGDIILLTDVV<I

Parental	HEDQWVGETVLQSTFSTQLLNLGSYSSIQPEECSSVVSDVVLQDLLAYVSSKHSYLRDLPPRQPQRVNSI
	HEDQWVG.TVLQSTFS.QLLNLGSYSSIQPEE.SS.VSDVVLQD.LAY.SSKHSYLRDLPPRQPQRVNSI
Retrocopy	HEDQWVGKTVLQSTFSSQLLNLGSYSSIQPEEYSSIVSDVVLQDFLAYMSSKHSYLRDLPPRQPQRVNSI

Parental	DFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWGPGAAWYPQLQR
	DFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWGPGAAWYPQLQR
Retrocopy	DFVELEHLQPDVLVHAVLRVVDFTILTEAVYSYRGQKQKKVMLTVEQAQDQHYVLVLWGPGAAWYPQLQR

Parental	KKGYIWEFKYLFVQRSYTLENLELHTTPWSSCECLFDDDIRAITFKAKFQKSAPSFVKISDLATHLEDKC
	KKGYIWEFKYLFVQ..YTLENLELHT.PWSSCECLFDDDI.AITFKAKFQK.APSFVKISDLAT.LEDKC
Retrocopy	KKGYIWEFKYLFVQHTYTLENLELHTVPWSSCECLFDDDITAITFKAKFQKNAPSFVKISDLATRLEDKC

Parental	SGVVLIKAQISELAFPITAAQKIALNAHSSLKSIFSSLPNIVYTGCAKCGLELETDENRIYK
	SGVVLIKAQISELAFPITAAQKIALNAHSSLKSIFSSLPNIVYTG.AKCGLELETDENRIYK
Retrocopy	SGVVLIKAQISELAFPITAAQKIALNAHSSLKSIFSSLPNIVYTGYAKCGLELETDENRIYK

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

RetrogeneDB ID:

retro_nleu_2157