RetrogeneDB - Retrocopy retro_ttru

                        
>retro_ttru_352
ATGAAGCCATTTTACCTCACCCAGCTGCCCGAGCTGCTTAAACTTTATTACCAGAAGCTCTTTCCCTAAGCCCAGTACTA

TCACTGGCTCAACTATGGCAGGGTGGTAAAGAATTACTTTCAACATCATGAGTTTTCATTCACATTGAAAGGTGATATTT

ACATTCATTACCAATCCTTCAACAACCAGAGTGATCTGGAAAAGGAGATGCAGAAAATGAATCCATACAAGATTGATATA

GGCTTAGTATAGTCCCACAGACCAAATCAACACAATACAGTGCATCTGGGAGCTTTCCGGGCTCAGGAAAAAGAACTGGT

GTTTGACATTGACATGACAGACTATGACGATGTGAGGAGACATTGTAGTTGTGCAGACATGTGTTCTAAGTGCTGGACCC

TCATGACGATGGCCACACACATCATCAACCGAGAATTGAAGGAGGACTTTGGATTTAAACATCATCTCTGGGTATATTCT

GGAAGGAGAGATGTTCATTTTTGGGTCTGTGATGAATCAGTTAGAAAACTGTCCTCTGCAGTACGTTCTGGGATATTTGA

ATATTTGAATCTTGTAAAGGGTGGTCAGGACGTTGAAAAGAAAGTTCATCTAAGTAACAAAAATTCACCCTTTTGTCAGA

AAATCTATAAACATAATGAAAAATACTTTGAAGAATATGCTTTGGTTGATTAAGATATTCTTGAGAATAAAGAAAGCTGG

GATAAGATTTTAACCCTTGTTCCTGAAACAATGCATGATGAACTTCAACAAAGCTTCCAAAAGCATCACGATTCACTTCA

GCATTGGGGGCATTTGAAGAAAGCAGCCAGCAGGTATCAGAATAACAGCAAAAATGAC

ORF - retro_ttru_352 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	84.72 %
Parental protein coverage:	69.59 %
Number of stop codons detected:	3
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalMEAFDPAELPELLKLYYRRLFPYAQYYRWLNYGGVVKNYFQHREFSFTLKDDIYIRYQSFNNQSDLEKEL
M..F....LPELLKLYY..LFP.AQYY.WLNYG.VVKNYFQH.EFSFTLK.DIYI.YQSFNNQSDLEKE.
RetrocopyMKPFYLTQLPELLKLYYQKLFP*AQYYHWLNYGRVVKNYFQHHEFSFTLKGDIYIHYQSFNNQSDLEKEM
ParentalQKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICSKCWTLMTMAIH
QKMNPYKIDIG.V.SHRPNQHNTV.LGAF.AQEKELVFDIDMTDYDDVRR.CS.AD.CSKCWTLMTMA.H
RetrocopyQKMNPYKIDIGLV*SHRPNQHNTVHLGAFRAQEKELVFDIDMTDYDDVRRHCSCADMCSKCWTLMTMATH
ParentalIIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSVVKGGQDVKKKVHLSE-KIH
II.R.LKEDFGFKH.LWVYSGRR.VH.WVCDESVRKLSSAVRSGI.EYL..VKGGQDV.KKVHLS..KIH
RetrocopyIINRELKEDFGFKHHLWVYSGRRDVHFWVCDESVRKLSSAVRSGIFEYLNLVKGGQDVEKKVHLSN>KIH
ParentalPFVRKSINIIL-KYFEDYALVDQDILENKESWDKILALVPETMHDELQQSFQKHHNSLQRWEHLKKAASR
PFVRKSINI...KYFE.YALVD.DILENKESWDKIL.LVPETMHDELQQSFQKHH.SLQ.W.HLKKAASR
RetrocopyPFVRKSINIMK<KYFEEYALVD*DILENKESWDKILTLVPETMHDELQQSFQKHHDSLQHWGHLKKAASR
ParentalCQNNSKND
.QNNSKND
RetrocopyYQNNSKND

                            

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

                        

RNA-Seq - click to see more details

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tursiops truncatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ttru_352 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_352 was not experimentally validated.

Retrocopy orthology:

Tursiops truncatus 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000015297	1 retrocopy	retro_ecab_447,
Homo sapiens	ENSG00000198056	1 retrocopy	retro_hsap_339,
Mustela putorius furo	ENSMPUG00000001603	1 retrocopy	retro_mputfur_587,
Nomascus leucogenys	ENSNLEG00000017443	1 retrocopy	retro_nleu_1780,
Oryctolagus cuniculus	ENSOCUG00000003458	1 retrocopy	retro_ocun_1265,
Procavia capensis	ENSPCAG00000007103	1 retrocopy	retro_pcap_174,
Pongo abelii	ENSPPYG00000004672	1 retrocopy	retro_pabe_356,
Pan troglodytes	ENSPTRG00000022987	1 retrocopy	retro_ptro_271,
Pteropus vampyrus	ENSPVAG00000008017	2 retrocopies	retro_pvam_153, retro_pvam_703,
Sus scrofa	ENSSSCG00000000408	1 retrocopy	retro_sscr_499,
Tupaia belangeri	ENSTBEG00000012998	1 retrocopy	retro_tbel_2255,
Tursiops truncatus	ENSTTRG00000002153	1 retrocopy	retro_ttru_352 ,

	RetrogeneDB ID:	retro_ttru_352
Retrocopy location	Organism:	*Dolphin (Tursiops truncatus)*
	Coordinates:	GeneScaffold_1963:56124..56982(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	PRIM1
	Ensembl ID:	ENSTTRG00000002153
	Aliases:	None
	Description:	primase, DNA, polypeptide 1 (49kDa) [Source:HGNC Symbol;Acc:9369]

Parental	MEAFDPAELPELLKLYYRRLFPYAQYYRWLNYGGVVKNYFQHREFSFTLKDDIYIRYQSFNNQSDLEKEL
	M..F....LPELLKLYY..LFP.AQYY.WLNYG.VVKNYFQH.EFSFTLK.DIYI.YQSFNNQSDLEKE.
Retrocopy	MKPFYLTQLPELLKLYYQKLFP*AQYYHWLNYGRVVKNYFQHHEFSFTLKGDIYIHYQSFNNQSDLEKEM

Parental	QKMNPYKIDIGAVYSHRPNQHNTVKLGAFQAQEKELVFDIDMTDYDDVRRCCSSADICSKCWTLMTMAIH
	QKMNPYKIDIG.V.SHRPNQHNTV.LGAF.AQEKELVFDIDMTDYDDVRR.CS.AD.CSKCWTLMTMA.H
Retrocopy	QKMNPYKIDIGLV*SHRPNQHNTVHLGAFRAQEKELVFDIDMTDYDDVRRHCSCADMCSKCWTLMTMATH

Parental	IIDRALKEDFGFKHRLWVYSGRRGVHCWVCDESVRKLSSAVRSGIVEYLSVVKGGQDVKKKVHLSE-KIH
	II.R.LKEDFGFKH.LWVYSGRR.VH.WVCDESVRKLSSAVRSGI.EYL..VKGGQDV.KKVHLS..KIH
Retrocopy	IINRELKEDFGFKHHLWVYSGRRDVHFWVCDESVRKLSSAVRSGIFEYLNLVKGGQDVEKKVHLSN>KIH

Parental	PFVRKSINIIL-KYFEDYALVDQDILENKESWDKILALVPETMHDELQQSFQKHHNSLQRWEHLKKAASR
	PFVRKSINI...KYFE.YALVD.DILENKESWDKIL.LVPETMHDELQQSFQKHH.SLQ.W.HLKKAASR
Retrocopy	PFVRKSINIMK<KYFEEYALVD*DILENKESWDKILTLVPETMHDELQQSFQKHHDSLQHWGHLKKAASR

Parental	CQNNSKND
	.QNNSKND
Retrocopy	YQNNSKND

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

RetrogeneDB ID:

retro_ttru_352