RetrogeneDB - Retrocopy retro_ecab

						
>retro_ecab_367
CCGGCCACAGGAGCGACGCGTGATAAAGAAACAGAAAGAAAAGTACCCAATCAAGGAAGGCCTGCCAAAAAGATAGAAAG

AAAACCTGGCAAGGTCGTTTCCTTTAAAGTTGATAGTGAAGAAAATACTTTGGAGTCACAAACCAATGTGACAAACGGAA

CGGATCCAGATGGAGTCTTATCAAAAATGGAAAAGTTACCTAAGTCAAATCCTGCAGCAGTGAAAGGGAGGCCATCCTTC

GCACCAGTAGATTTCGTATTTCGGCCTCCAGATGGTCTGAAGAGCTATGAGATAACACCTAGGAAGCCCACAAAAACCAC

TGCGTGGACGCCCGCTTACAGCTGCAGCTCTTTAAACACGGAAGTTGATAAGGCTCTAGAAGCAACAAAAGAAATTTTGG

CACAGAAATGTAAACCTTCAGCACATCAAGATTACGATGAATTTCGCCGTCCTTTGCGCTCCCTAGCAGTCGGGAGCACA

GATCGTGTCTTAAAGAAAAATGAAACTACTACTGAAAATCTACATGGCCTTCCAATAAAAGAAGTCCCATCACTTGAAAT

AAATGAGGATCAGACATCTCAGCAACCACACGTGCTGTATTTCAGAAATATTCTCCAGTCAGAAACTGAAAAACTAACTT

CACACTGCCTTGAGTGGGAAAGGAAGCTTGAATTGGACATTCCAGATGAAGCCAAAGACCTTATTCGCCTGGCAGTTGGT

CAAACAAGACTCCTTATGAAAGAAAGGTTCAAACAGTTTGAAGAACTGGTGGACAATTGTGACTATAAACGAGGAGAAAA

GGATACCACCTGTACAGACCTGGATGGCTTTTGGGATATGGCTAGCCTTCAGATATGGGATGTAAACCAAAAATTCAACA

ATCTGACCAAACTGGAGGAGTGTGAATGGCAAAACAATAATAATACAAGCAAAAAAGTCTTTCAGAAAAAAGTTGTTTCG

GGTATAGCAAGTAAACCAAAACAGGACGATGCTGGGAGAATTGCAGCCAGAAGTCGCCTCGCTGCTGTGAAGAAGGCAGT

GAGAGAGAGGATGCACGGGGAGAGCAGGCCGAGGCCGAGGGCTCTGCAGCGCCGAAGGAAGTTGATCAAATAGTGTTTGA

CGCTGGATTTTTTAGAATTGAAAGTCCCGTTAAATCGTTCTCA

ORF - retro_ecab_367 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	91.26 %
Parental protein coverage:	61.98 %
Number of stop codons detected:	0
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalPATRAARDNETERKVPNQGRPAKKIERKPGKVVSFKVDSEENTLESQTIVTNGMDPDGVLSKMEKLPKTN
		PAT.A.RD.ETERKVPNQGRPAKKIERKPGKVVSFKVDSEENTLESQT.VTNG.DPDGVLSKMEKLPK.N
RetrocopyPATGATRDKETERKVPNQGRPAKKIERKPGKVVSFKVDSEENTLESQTNVTNGTDPDGVLSKMEKLPKSN
ParentalPAAVKGRPSFAPVDFVFRPPDGLKSYEITPRTPTSTAAWTPTYSCSSLNTEVDKAPEATKETLAQKCKPS
		PAAVKGRPSFAPVDFVFRPPDGLKSYEITPR.PT.T.AWTP.YSCSSLNTEVDKA.EATKE.LAQKCKPS
RetrocopyPAAVKGRPSFAPVDFVFRPPDGLKSYEITPRKPTKTTAWTPAYSCSSLNTEVDKALEATKEILAQKCKPS
ParentalAHQECDGWRRPLSSLAVGSTDRVLNKNETTTENLHGLPIKEVPSLEINEDQTSQPRHVLYFRSILQSETE
		AHQ..D..RRPL.SLAVGSTDRVL.KNETTTENLHGLPIKEVPSLEINEDQTSQ..HVLYFR.ILQSETE
RetrocopyAHQDYDEFRRPLRSLAVGSTDRVLKKNETTTENLHGLPIKEVPSLEINEDQTSQQPHVLYFRNILQSETE
ParentalKLTSHCLEWERKLELDVPDEAKDLIRLAVGQTRLLMKERFKQFEELVDDCEYKRGEKDTTCADLDGFWDM
		KLTSHCLEWERKLELD.PDEAKDLIRLAVGQTRLLMKERFKQFEELVD.C.YKRGEKDTTC.DLDGFWDM
RetrocopyKLTSHCLEWERKLELDIPDEAKDLIRLAVGQTRLLMKERFKQFEELVDNCDYKRGEKDTTCTDLDGFWDM
ParentalVSLQVRDVNQKFNNLTKLEECEWQNNNNTSKKVFQKKVVSGLASKPKQDDAGRIAARSRLAAVKKAVRER
		.SLQ..DVNQKFNNLTKLEECEWQNNNNTSKKVFQKKVVSG.ASKPKQDDAGRIAARSRLAAVKKAVRER
RetrocopyASLQIWDVNQKFNNLTKLEECEWQNNNNTSKKVFQKKVVSGIASKPKQDDAGRIAARSRLAAVKKAVRER
ParentalMQ-RGEQAGAAGSAVPKEVDQIVFDAGFFRIESPVKSFS
		M..RGEQA.A.GSA.PKEVDQIVFDAGFFRIESPVKSFS
RetrocopyMH<RGEQAEAEGSAAPKEVDQIVFDAGFFRIESPVKSFS

							

							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
SRP021940_articular_cartilage	1 .77 RPM	0 .06 RPM
SRP021940_cerebellum	7 .58 RPM	0 .31 RPM
SRP021940_embryo	2 .17 RPM	22 .45 RPM
SRP021940_placental_villous	0 .72 RPM	2 .26 RPM
SRP021940_synovial_membrane	1 .65 RPM	2 .31 RPM
SRP021940_testis	1 .09 RPM	16 .75 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_367 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_367 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ecab_367 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007001	1 retrocopy	retro_amel_831,
Equus caballus	ENSECAG00000008655	1 retrocopy	retro_ecab_367 ,

	RetrogeneDB ID:	retro_ecab_367
Retrocopy location	Organism:	*Horse (Equus caballus)*
	Coordinates:	16:73233929..73235092(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSECAG00000023737
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	DLGAP5
	Ensembl ID:	ENSECAG00000008655
	Aliases:	None
	Description:	discs, large (Drosophila) homolog-associated protein 5 [Source:HGNC Symbol;Acc:16864]

Parental	PATRAARDNETERKVPNQGRPAKKIERKPGKVVSFKVDSEENTLESQTIVTNGMDPDGVLSKMEKLPKTN
	PAT.A.RD.ETERKVPNQGRPAKKIERKPGKVVSFKVDSEENTLESQT.VTNG.DPDGVLSKMEKLPK.N
Retrocopy	PATGATRDKETERKVPNQGRPAKKIERKPGKVVSFKVDSEENTLESQTNVTNGTDPDGVLSKMEKLPKSN

Parental	PAAVKGRPSFAPVDFVFRPPDGLKSYEITPRTPTSTAAWTPTYSCSSLNTEVDKAPEATKETLAQKCKPS
	PAAVKGRPSFAPVDFVFRPPDGLKSYEITPR.PT.T.AWTP.YSCSSLNTEVDKA.EATKE.LAQKCKPS
Retrocopy	PAAVKGRPSFAPVDFVFRPPDGLKSYEITPRKPTKTTAWTPAYSCSSLNTEVDKALEATKEILAQKCKPS

Parental	AHQECDGWRRPLSSLAVGSTDRVLNKNETTTENLHGLPIKEVPSLEINEDQTSQPRHVLYFRSILQSETE
	AHQ..D..RRPL.SLAVGSTDRVL.KNETTTENLHGLPIKEVPSLEINEDQTSQ..HVLYFR.ILQSETE
Retrocopy	AHQDYDEFRRPLRSLAVGSTDRVLKKNETTTENLHGLPIKEVPSLEINEDQTSQQPHVLYFRNILQSETE

Parental	KLTSHCLEWERKLELDVPDEAKDLIRLAVGQTRLLMKERFKQFEELVDDCEYKRGEKDTTCADLDGFWDM
	KLTSHCLEWERKLELD.PDEAKDLIRLAVGQTRLLMKERFKQFEELVD.C.YKRGEKDTTC.DLDGFWDM
Retrocopy	KLTSHCLEWERKLELDIPDEAKDLIRLAVGQTRLLMKERFKQFEELVDNCDYKRGEKDTTCTDLDGFWDM

Parental	VSLQVRDVNQKFNNLTKLEECEWQNNNNTSKKVFQKKVVSGLASKPKQDDAGRIAARSRLAAVKKAVRER
	.SLQ..DVNQKFNNLTKLEECEWQNNNNTSKKVFQKKVVSG.ASKPKQDDAGRIAARSRLAAVKKAVRER
Retrocopy	ASLQIWDVNQKFNNLTKLEECEWQNNNNTSKKVFQKKVVSGIASKPKQDDAGRIAARSRLAAVKKAVRER

Parental	MQ-RGEQAGAAGSAVPKEVDQIVFDAGFFRIESPVKSFS
	M..RGEQA.A.GSA.PKEVDQIVFDAGFFRIESPVKSFS
Retrocopy	MH<RGEQAEAEGSAAPKEVDQIVFDAGFFRIESPVKSFS

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

RetrogeneDB ID:

retro_ecab_367