RetrogeneDB - Retrocopy retro_rnor

	RetrogeneDB ID:	retro_rnor_1025
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	14:99238845..99239232(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSRNOG00000030181
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	Carhsp1
	Ensembl ID:	ENSRNOG00000002610
	Aliases:	Carhsp1, Crhsp-24, Crhsp24
	Description:	Calcium-regulated heat stable protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9WU49]

Retrocopy-Parental alignment summary:

						
>retro_rnor_1025
ATGTCATCTGAGTCTCCTTCGCTGCCACCATAGCCCCCACACATGAGACTTCTGTAGGGCTATTGGATACCCCTTGTGCC

CAGCATTGTTCTCCATCCACGATGAAGGGCAATGTGGTCCCTAGCCCTCTGCCTACATGCCAGACACTTCTCAGTGATGG

TGCAGGCTTTGCAGTGCCCTGTCTACAAGGGAGACTGTAAATGCTTCTGCCGTTCCAAGGGTCATGGCTTCATCATCCTT

GGTGATGGTGGTCCTGACATCTTCTTGCACATCTCTGATGTGGAAGGGGAGTATGTTCCGGTGGAAGGTGATGAGGTCAT

CTATGAGGTGTGCTCTATCCTGCCCAAGAATGAGAAACTCACCCACCTGGCACCAGGGACCACACAT

ORF - retro_rnor_1025 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	67.67 %
Parental protein coverage:	88.44 %
Number of stop codons detected:	1
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalMSSEPPP-PPQPP-THQTSIGLLDTPRARDRSPSPLRGNVVPSPLPTRRTRT-FSATVRASQGPVYKGVC
		MSSE.P..PP.PP.TH.TS.GLLDTP.A...SPS...GNVV..P.P.....T.FS..V.A.Q.PVYKG.C
RetrocopyMSSESPSLPP*PP<THETSVGLLDTPCAQHCSPSTMKGNVV--PSPLPTCQT>FSVMVQALQCPVYKGDC
ParentalKCFCRSKGHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIPPKNEKLQAVEVVITH
		KCFCRSKGHGFI...DGGPDIFLHISDVEGEYVPVEGDEV.Y..CSI.PKNEKL.......TH
RetrocopyKCFCRSKGHGFIILGDGGPDIFLHISDVEGEYVPVEGDEVIYEVCSILPKNEKLTHLAPGTTH

							

							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
SRP017611_brain	0 .00 RPM	32 .50 RPM
SRP017611_kidney	0 .00 RPM	57 .85 RPM
SRP017611_liver	0 .00 RPM	134 .07 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_1025 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1025 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_1025 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017286	1 retrocopy	retro_cjac_194,
Macropus eugenii	ENSMEUG00000016403	1 retrocopy	retro_meug_1949,
Monodelphis domestica	ENSMODG00000005721	1 retrocopy	retro_mdom_12,
Mus musculus	ENSMUSG00000008393	1 retrocopy	retro_mmus_88,
Rattus norvegicus	ENSRNOG00000002610	1 retrocopy	retro_rnor_1025 ,

Parental	MSSEPPP-PPQPP-THQTSIGLLDTPRARDRSPSPLRGNVVPSPLPTRRTRT-FSATVRASQGPVYKGVC
	MSSE.P..PP.PP.TH.TS.GLLDTP.A...SPS...GNVV..P.P.....T.FS..V.A.Q.PVYKG.C
Retrocopy	MSSESPSLPP*PP<THETSVGLLDTPCAQHCSPSTMKGNVV--PSPLPTCQT>FSVMVQALQCPVYKGDC

Parental	KCFCRSKGHGFITPADGGPDIFLHISDVEGEYVPVEGDEVTYKMCSIPPKNEKLQAVEVVITH
	KCFCRSKGHGFI...DGGPDIFLHISDVEGEYVPVEGDEV.Y..CSI.PKNEKL.......TH
Retrocopy	KCFCRSKGHGFIILGDGGPDIFLHISDVEGEYVPVEGDEVIYEVCSILPKNEKLTHLAPGTTH

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

RetrogeneDB ID:

retro_rnor_1025