RetrogeneDB - Retrocopy retro_itri

	RetrogeneDB ID:	retro_itri_1084
Retrocopy location	Organism:	*Squirrel (Ictidomys tridecemlineatus)*
	Coordinates:	JH393372.1:1588250..1588645(-)
	Located in intron of:	ENSSTOG00000003491
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	NDUFB11
	Ensembl ID:	ENSSTOG00000026821
	Aliases:	None
	Description:	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11, 17.3kDa [Source:HGNC Symbol;Acc:20372]

Retrocopy-Parental alignment summary:

						
>retro_itri_1084
AGTGTCCACGTTTGCTGGGAATCCAGCTCCTCCAGAGCTATGGTTGCCCCATCTGCTTCAGTGAGAAAGAGGAAATAACC

AGAAATAACCACACACTGGTGGGAGGACCCAGATCCTGAGGACAAAAACCTCTATGAGAAGAATCCAGACTCCCATAGTT

ATGACAATGGTCTGCTGTGAGTCTCTGGAACACTCAGGTGATCTTCTCTGGCTTCTCTATCATCCTGGTCTTTGTCAGTT

CCTTTGTGACTTATCTGCCTGACTATGGGATGCAAGAGTGGGCCTGATGGGAAACTGAGAGGCTTGTGAAACACCAAGAG

GCCAACAGCCTCCCAATCTTGGAAGAGGAAGAATATTGTTGCTTTGGCCCCAATGATATTCAGCTATTGGAGGAT

ORF - retro_itri_1084 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	59.7 %
Parental protein coverage:	84.31 %
Number of stop codons detected:	2
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalAARVRWESSSSRAVVAPSAVAGKRP-PEPTMRWQEDPEPEDENLYEKNPDSHGYDKD-PVVDLWNMRVIF
		...V.WESSSSRA.VAPSA...KR..PE.T..W.EDP.PED.NLYEKNPDSH.YD.....V.LWN..VIF
RetrocopySVHVCWESSSSRAMVAPSASVRKRK*PEITTHWWEDPDPEDKNLYEKNPDSHSYDNG<SAVSLWNTQVIF
ParentalFFGVSIVLVLGTTFVAYLPDYSMREWARREAERLVKYREANGLPVMESN---CFDPSKIQLPDD
		..G.SI.LV....FV.YLPDY.M.EWA..E.ERLVK..EAN.LP..E.....CF.P..IQL..D
RetrocopyS-GFSIILVFVSSFVTYLPDYGMQEWA*WETERLVKHQEANSLPILEEEEYCCFGPNDIQLLED

							

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

						

RNA-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_itri_1084 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_1084 was not experimentally validated.

Retrocopy orthology:

Ictidomys tridecemlineatus 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000147123	1 retrocopy	retro_hsap_912,
Macaca mulatta	ENSMMUG00000017422	2 retrocopies	retro_mmul_1116, retro_mmul_830,
Monodelphis domestica	ENSMODG00000018491	1 retrocopy	retro_mdom_1063,
Mus musculus	ENSMUSG00000031059	2 retrocopies	retro_mmus_245, retro_mmus_2602,
Pongo abelii	ENSPPYG00000020284	1 retrocopy	retro_pabe_788,
Pan troglodytes	ENSPTRG00000021836	1 retrocopy	retro_ptro_633,
Rattus norvegicus	ENSRNOG00000008329	1 retrocopy	retro_rnor_151,
Ictidomys tridecemlineatus	ENSSTOG00000026821	1 retrocopy	retro_itri_1084 ,

Parental	AARVRWESSSSRAVVAPSAVAGKRP-PEPTMRWQEDPEPEDENLYEKNPDSHGYDKD-PVVDLWNMRVIF
	...V.WESSSSRA.VAPSA...KR..PE.T..W.EDP.PED.NLYEKNPDSH.YD.....V.LWN..VIF
Retrocopy	SVHVCWESSSSRAMVAPSASVRKRK*PEITTHWWEDPDPEDKNLYEKNPDSHSYDNG<SAVSLWNTQVIF

Parental	FFGVSIVLVLGTTFVAYLPDYSMREWARREAERLVKYREANGLPVMESN---CFDPSKIQLPDD
	..G.SI.LV....FV.YLPDY.M.EWA..E.ERLVK..EAN.LP..E.....CF.P..IQL..D
Retrocopy	S-GFSIILVFVSSFVTYLPDYGMQEWA*WETERLVKHQEANSLPILEEEEYCCFGPNDIQLLED

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

RetrogeneDB ID:

retro_itri_1084