RetrogeneDB - Retrocopy retro_itri

						
>retro_itri_550
ATGGCTGTCCACCCACCGCCCCCACCGGACAAGCTGGAGGGAGGTGGCGGCCCTACATCGGGGGCCCCCTGCTCCACCCA

GCACCGGGAGGAAGCAGGGCAAGGCCGGTTTGAAAATGAAGAGCCCAGAAAAGAAGCGAAGAAAGTCAAATACTCAGGGC

CCTGTTTACTCACGGCTGACGGAGTTTGCACCACCCCCACTACCCCCGACTCCCATGGTGGATCATCTGGTTGCATCCAA

CTCTTTTGAGGGTGACTTCGGAGCCCCTAAGGTGGCTGCGCGGCCCCTCCATTCCTGCGCAGTCCTGTGCTCTTTGGAAG

CTTCCGTGTATTAGGGGGCATGACAGGCCAGGTACCCTCAGGCTGTGGAGGGGTCCCCAGACACTTGCCGATAAACCCCC

CTTTCCCTCCTAATCCTATGGGACCTGCTTTCAACATGCCCCCCAGGGCCCTGGCTACCCACCCCCAGGCAACATGAACT

TTCCCAGTCAACCCTTCAGCCAGCCTCTGGGTCAAAACTTCAGCGCTCCAGGTGGGCAGATGATGCCAGGCCCAGTGGGG

GATTTGGCCCCACGATCTCACCCACCATGGGACAGCCTCCCAGAGGGAAACTGGGCCCTCCTTCTCTCTCCCAGCGCTTT

GCCCAGCCAGGTGTGCCTTTTGGCCCTTCTCCTCTACAGAGACCCGGTCAGGGGCTCCCCAGCCTACCCCCCAACACAAA

TCCCTTCCCTGGTCCAGACCCCGGCTTTCCTGGCCCTGGTGGTGAGGATGGGGGAAGCCCTTGAATCCACCTGCTCCCAC

TGCTTTTCCCCAGGAGCCTCATTCAGGCTCGCCAGCTGCTGCTGTTAATGGGAATCAGCCCAGTTTCCCCCCAAACAGCA

GTGGACGGGTGGTGGCACTCCAGATGCCAACAGCTTAGCACCCCCTGGCAAGGCAGATGGGAGTTTAGGGCCCCAGCCTC

CCCCAGGCCTGCGTACCCATGTGGTGCCTGTCGGAGCGAGGTGAATGACGACCAGGATGCTGTCTTGTGTGAGGCCTCCT

GCCAGAAGTGGTGCCACCGGAGTGCACAGGCATGACTGAGAGCGTGACCACTGAAGTCTCTGCTGTCTGGGCCTGTGATC

TCTGCCTCAAGACCAAGGAGATCCAGTCTGTCTACATCCGCGAGGGCAAGGGGCAGCTGGTGGCTGCTAATGATGGG

ORF - retro_itri_550 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	84.93 %
Parental protein coverage:	100. %
Number of stop codons detected:	0
Number of frameshifts detected	8

Retrocopy - Parental Gene Alignment:

									ParentalMAASAPPPPDKLEG-GGGPAP-PPAPPSTGRKQGKAGLQMKSPEKKRRKSNTQGPAYSHLTEFAPPP---
		MA...PPPPDKLEG.GG.....PPAPPSTGRKQGKAGL.MKSPEKKRRKSNTQGP.YS.LTEFAPPP...
RetrocopyMAVHPPPPPDKLEGGGGPTSG>PPAPPSTGRKQGKAGLKMKSPEKKRRKSNTQGPVYSRLTEFAPPPLPP
ParentalTPMVDHLVASNPFEDDFGAPKV-GGAAPPFLGSPVPFGSFRVQGGMAGQVPPGYGTGGGGGPQTLRRQPP
		TPMVDHLVASN.FE.DFGAPKV.G.AAPPFL.SPV.FGSFRV.GGM.GQVP.G.G....G.P..L...P.
RetrocopyTPMVDHLVASNSFEGDFGAPKV<GCAAPPFLRSPVLFGSFRVLGGMTGQVPSGCG----GVPRHLPINP-
ParentalPFPPNPMGPAFNMP-PQGPGYPPPGNMNFPSQPFSQPLGQNFSPPGGQMM--PVG-GFGTMISPTMGQPP
		PFPPNPMGPAFNMP.PQGPGYPPPGNMNFPSQPFSQPLGQNFS.PGGQMM..PVG.GFG..ISPTMGQPP
RetrocopyPFPPNPMGPAFNMP<PQGPGYPPPGNMNFPSQPFSQPLGQNFSAPGGQMMPGPVG<GFGPTISPTMGQPP
ParentalRGELGPPSLPQRFAQPGVPFGPSPLQRPGQGLPSLPPNTSPFPGPDPGFPGPGGEDG-GKPLNPPAPTAF
		RG.LGPPSL.QRFAQPGVPFGPSPLQRPGQGLPSLPPNT.PFPGPDPGFPGPGGEDG.GKPLNPPAPTAF
RetrocopyRGKLGPPSLSQRFAQPGVPFGPSPLQRPGQGLPSLPPNTNPFPGPDPGFPGPGGEDG<GKPLNPPAPTAF
ParentalPQEPHSGSPAAAVNGNQPSFPPNSSGR-GGGTPDANSLAPPGKAGGGSGPQPPPGL-VYPCGACRSEVND
		PQEPHSGSPAAAVNGNQPSFPPNSSGR.GGGTPDANSLAPPGKA.G..GPQPPPGL..YPCGACRSEVND
RetrocopyPQEPHSGSPAAAVNGNQPSFPPNSSGR<GGGTPDANSLAPPGKADGSLGPQPPPGL<AYPCGACRSEVND
ParentalDQDAILCEASCQKWFHR-ECTGMTESAYGLLTTEASAVWACDLCLKTKEIQSVYIREGMGQLVAANDG
		DQDA.LCEASCQKW.HR.ECTGMTES.....TTE.SAVWACDLCLKTKEIQSVYIREG.GQLVAANDG
RetrocopyDQDAVLCEASCQKWCHR<ECTGMTES----VTTEVSAVWACDLCLKTKEIQSVYIREGKGQLVAANDG

							

							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_550 retrocopy.

TSS - click to see more details

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_itri_550 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000047824	1 retrocopy	retro_mmus_693,
Ictidomys tridecemlineatus	ENSSTOG00000000053	1 retrocopy	retro_itri_550 ,

	RetrogeneDB ID:	retro_itri_550
Retrocopy location	Organism:	*Squirrel (Ictidomys tridecemlineatus)*
	Coordinates:	JH393300.1:16723326..16724523(-)
	Located in intron of:	ENSSTOG00000005956
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	PYGO2
	Ensembl ID:	ENSSTOG00000000053
	Aliases:	None
	Description:	pygopus homolog 2 (Drosophila) [Source:HGNC Symbol;Acc:30257]

Parental	MAASAPPPPDKLEG-GGGPAP-PPAPPSTGRKQGKAGLQMKSPEKKRRKSNTQGPAYSHLTEFAPPP---
	MA...PPPPDKLEG.GG.....PPAPPSTGRKQGKAGL.MKSPEKKRRKSNTQGP.YS.LTEFAPPP...
Retrocopy	MAVHPPPPPDKLEGGGGPTSG>PPAPPSTGRKQGKAGLKMKSPEKKRRKSNTQGPVYSRLTEFAPPPLPP

Parental	TPMVDHLVASNPFEDDFGAPKV-GGAAPPFLGSPVPFGSFRVQGGMAGQVPPGYGTGGGGGPQTLRRQPP
	TPMVDHLVASN.FE.DFGAPKV.G.AAPPFL.SPV.FGSFRV.GGM.GQVP.G.G....G.P..L...P.
Retrocopy	TPMVDHLVASNSFEGDFGAPKV<GCAAPPFLRSPVLFGSFRVLGGMTGQVPSGCG----GVPRHLPINP-

Parental	PFPPNPMGPAFNMP-PQGPGYPPPGNMNFPSQPFSQPLGQNFSPPGGQMM--PVG-GFGTMISPTMGQPP
	PFPPNPMGPAFNMP.PQGPGYPPPGNMNFPSQPFSQPLGQNFS.PGGQMM..PVG.GFG..ISPTMGQPP
Retrocopy	PFPPNPMGPAFNMP<PQGPGYPPPGNMNFPSQPFSQPLGQNFSAPGGQMMPGPVG<GFGPTISPTMGQPP

Parental	RGELGPPSLPQRFAQPGVPFGPSPLQRPGQGLPSLPPNTSPFPGPDPGFPGPGGEDG-GKPLNPPAPTAF
	RG.LGPPSL.QRFAQPGVPFGPSPLQRPGQGLPSLPPNT.PFPGPDPGFPGPGGEDG.GKPLNPPAPTAF
Retrocopy	RGKLGPPSLSQRFAQPGVPFGPSPLQRPGQGLPSLPPNTNPFPGPDPGFPGPGGEDG<GKPLNPPAPTAF

Parental	PQEPHSGSPAAAVNGNQPSFPPNSSGR-GGGTPDANSLAPPGKAGGGSGPQPPPGL-VYPCGACRSEVND
	PQEPHSGSPAAAVNGNQPSFPPNSSGR.GGGTPDANSLAPPGKA.G..GPQPPPGL..YPCGACRSEVND
Retrocopy	PQEPHSGSPAAAVNGNQPSFPPNSSGR<GGGTPDANSLAPPGKADGSLGPQPPPGL<AYPCGACRSEVND

Parental	DQDAILCEASCQKWFHR-ECTGMTESAYGLLTTEASAVWACDLCLKTKEIQSVYIREGMGQLVAANDG
	DQDA.LCEASCQKW.HR.ECTGMTES.....TTE.SAVWACDLCLKTKEIQSVYIREG.GQLVAANDG
Retrocopy	DQDAVLCEASCQKWCHR<ECTGMTES----VTTEVSAVWACDLCLKTKEIQSVYIREGKGQLVAANDG

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

RetrogeneDB ID:

retro_itri_550