RetrogeneDB - Retrocopy retro_ecab

						
>retro_ecab_95
ATGGGGAAGCGAGATAATCGGGTGGCATATATGAATCCTATAGCGATGGCCAGATGGAGGGGCCCAACTCAATCTGCAGG

TCCAACAATACAAGATTATCTGAATCGACCAAGGCCCACATGGGAAGAAGTGAAGAAACAATTAGAAAATAAAAAGAAAG

GCTCCAAGGCATTAGCTGAATTTGAAGAAAAAATGAACGAGAATTGGAAGAAAGAACTAGAAGAAAGCAGAGAGAAATTA

TTAAGTGGAAATGAGAGTTCATCCAAAAAAAGAGAGAGAAAGAAAAAGAAAAAGAAGAAGTCTTCTCGGTCTTCGTCATC

TTCTTCATCAAGCTCTGATTCTTCAAGCAGTTCTTCAGATTCTGAAGATGAGGAAAAGAAACAAGGTAAAAAGAGAAAGA

AAAAGAAGAATCGTTCACACAAATCATCACAAAGCTCTACATATGAATCTGAGTCAGAGAGCAAGGAATATGTAAAAAAG

AAAAAGAAGTCACAAGATGAAACAGAGAAAGAAAAGGATGTCAGAAGTCTCAGCAAAAAAAGAAAGAAGACGTATCCTGA

GGATAAACCTTTATCATCGGAGTCCTCATCAGAATCAGATTATAAAGAGGAGGTACAAGCAAAAAAGAAGAGAAGATGTG

AAGAGCAAGAAAAAGCAATGGAAAAAGCAAAGAAGAAGAAAAAAAAACAGCACAAGAAACATAGTAAGAAGAAGAAAAAG

AAGTCAGGTTCAAGTCACAAGTCGGAATAA

ORF - retro_ecab_95 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	81.63 %
Parental protein coverage:	97.98 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalMGKRDNRVAYMNPIAMARSRGPIQSSGPTIQDYLNRPRPTWEEVKEQLEKKKKGSKALAEFEEKMNENWK
		MGKRDNRVAYMNPIAMAR.RGP.QS.GPTIQDYLNRPRPTWEEVK.QLE.KKKGSKALAEFEEKMNENWK
RetrocopyMGKRDNRVAYMNPIAMARWRGPTQSAGPTIQDYLNRPRPTWEEVKKQLENKKKGSKALAEFEEKMNENWK
ParentalKELEKHREKLLSGSESSSKKRQRKKKEKKKSGRYSSSSSSSSDSSSSSSGSEDEDKKQGKRKKKKKNRSH
		KELE..REKLLSG.ESSSKKR.RKKK.KKKS.R.SSSSSSSSDSSSSSS.SEDE.KKQGK..KKKKNRSH
RetrocopyKELEESREKLLSGNESSSKKRERKKKKKKKSSRSSSSSSSSSDSSSSSSDSEDEEKKQGKKRKKKKNRSH
ParentalKSSESSISETESDSKDSLKKKKKSKDATEKEKDIKGLSKKR-KMYPEDKPLSSESLSESDYIEEVRAKKK
		KSS.SS..E.ES.SK...KKKKKS.D.TEKEKD...LSKKR.K.YPEDKPLSSES.SESDY.EEV.AKKK
RetrocopyKSSQSSTYESESESKEYVKKKKKSQDETEKEKDVRSLSKKRKKTYPEDKPLSSESSSESDYKEEVQAKKK
ParentalKSSEEREKTTEKTKKKKK--HKKHSKKKKKKAASS
		...EE.EK..EK.KKKKK..HKKHSKKKKKK..SS
RetrocopyRRCEEQEKAMEKAKKKKKKQHKKHSKKKKKKSGSS

							

							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	0 .41 RPM	0 .35 RPM
SRP021940_cerebellum	0 .21 RPM	1 .40 RPM
SRP021940_embryo	0 .84 RPM	5 .65 RPM
SRP021940_placental_villous	0 .10 RPM	1 .88 RPM
SRP021940_synovial_membrane	0 .14 RPM	2 .75 RPM
SRP021940_testis	0 .06 RPM	1 .15 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_95 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_95 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ecab_95 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_49
Macaca mulatta	retro_mmul_226

Parental genes homology:

Parental genes homology involve 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007438	1 retrocopy	retro_amel_102,
Callithrix jacchus	ENSCJAG00000013910	3 retrocopies	retro_cjac_1084, retro_cjac_1163, retro_cjac_4095,
Equus caballus	ENSECAG00000026810	1 retrocopy	retro_ecab_95 ,
Homo sapiens	ENSG00000234545	4 retrocopies	retro_hsap_2336, retro_hsap_3179, retro_hsap_55, retro_hsap_577,
Loxodonta africana	ENSLAFG00000029755	1 retrocopy	retro_lafr_594,
Myotis lucifugus	ENSMLUG00000005933	1 retrocopy	retro_mluc_2301,
Macaca mulatta	ENSMMUG00000019802	4 retrocopies	retro_mmul_1415, retro_mmul_226, retro_mmul_420, retro_mmul_765,
Mus musculus	ENSMUSG00000058503	2 retrocopies	retro_mmus_3481, retro_mmus_3519,
Nomascus leucogenys	ENSNLEG00000015333	1 retrocopy	retro_nleu_14,
Pongo abelii	ENSPPYG00000025825	1 retrocopy	retro_pabe_225,
Rattus norvegicus	ENSRNOG00000009163	1 retrocopy	retro_rnor_2891,
Sus scrofa	ENSSSCG00000015317	1 retrocopy	retro_sscr_49,
Ictidomys tridecemlineatus	ENSSTOG00000028195	1 retrocopy	retro_itri_12,
Tupaia belangeri	ENSTBEG00000011674	1 retrocopy	retro_tbel_1,

	RetrogeneDB ID:	retro_ecab_95
Retrocopy location	Organism:	*Horse (Equus caballus)*
	Coordinates:	X:73374980..73375730(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSECAG00000003733
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	FAM133B
	Ensembl ID:	ENSECAG00000026810
	Aliases:	None
	Description:	family with sequence similarity 133, member B [Source:HGNC Symbol;Acc:28629]

Parental	MGKRDNRVAYMNPIAMARSRGPIQSSGPTIQDYLNRPRPTWEEVKEQLEKKKKGSKALAEFEEKMNENWK
	MGKRDNRVAYMNPIAMAR.RGP.QS.GPTIQDYLNRPRPTWEEVK.QLE.KKKGSKALAEFEEKMNENWK
Retrocopy	MGKRDNRVAYMNPIAMARWRGPTQSAGPTIQDYLNRPRPTWEEVKKQLENKKKGSKALAEFEEKMNENWK

Parental	KELEKHREKLLSGSESSSKKRQRKKKEKKKSGRYSSSSSSSSDSSSSSSGSEDEDKKQGKRKKKKKNRSH
	KELE..REKLLSG.ESSSKKR.RKKK.KKKS.R.SSSSSSSSDSSSSSS.SEDE.KKQGK..KKKKNRSH
Retrocopy	KELEESREKLLSGNESSSKKRERKKKKKKKSSRSSSSSSSSSDSSSSSSDSEDEEKKQGKKRKKKKNRSH

Parental	KSSESSISETESDSKDSLKKKKKSKDATEKEKDIKGLSKKR-KMYPEDKPLSSESLSESDYIEEVRAKKK
	KSS.SS..E.ES.SK...KKKKKS.D.TEKEKD...LSKKR.K.YPEDKPLSSES.SESDY.EEV.AKKK
Retrocopy	KSSQSSTYESESESKEYVKKKKKSQDETEKEKDVRSLSKKRKKTYPEDKPLSSESSSESDYKEEVQAKKK

Parental	KSSEEREKTTEKTKKKKK--HKKHSKKKKKKAASS
	...EE.EK..EK.KKKKK..HKKHSKKKKKK..SS
Retrocopy	RRCEEQEKAMEKAKKKKKKQHKKHSKKKKKKSGSS

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

RetrogeneDB ID:

retro_ecab_95