RetrogeneDB ID: retro_rnor_1998

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:178606797..178607234(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Pigx
• Ensembl ID: ENSRNOG00000033623
• Aliases: Pigx, RGD1307289
• Description: phosphatidylinositol-glycan biosynthesis class X protein precursor [Source:RefSeq peptide;Acc:NP_001094121]

Sequence

>retro_rnor_1998
AGTTTTAATCTAGAAGCCCCCAGCTATTTGTCCACAGAGTCTGTGGTCCTCATTTATGCCCGGCAGGACGCACAGTGCAT
CGACTGCTTCCAGGCCTTCCTACCTGTGCACTATCGATATCACCGTCCACATAAGAAGGATGGAGACACCCTCATTGTGG
TCAACAACCCTGACTTACTGATGCACTGTGACTAAGAGTTCCCAATTTTGAAATGCTAGGCTCAGTCAGAAGTAGCAGCT
CCTTGTTCTTTGAAGAGTGAGGAGATCTGCCAGTGGAAAAACATGCAGTACAAATCAATACTTAAGAATTGACAGTCCAG
GTGCCAGTGGGACTGACTATACACACCTCCTTAGTGTGCTCCGTGACACTGCTCACTACGGTTCTGTGTTCTACTCTGAT
CCTTTTAGCTGTTTTCAAATATGGCCATTTTTCCCTG

Alignment

ORF - retro_rnor_1998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.6 %
• Parental protein coverage: 55.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SFNLEAPSYLSTESAVLIYARQDAQCIDCFQAFLPVHYRYHRPHKKDGDTLIVVNNPDLLMHCDQEFPIL
          SFNLEAPSYLSTES.VLIYARQDAQCIDCFQAFLPVHYRYHRPHKKDGDTLIVVNNPDLLMHCD.EFPIL
Retrocopy SFNLEAPSYLSTESVVLIYARQDAQCIDCFQAFLPVHYRYHRPHKKDGDTLIVVNNPDLLMHCD*EFPIL

Parental  KCWAQSEVAAPCSLKSEEICQWKNMQYKSILKN-LTVQVPVGLTIHTSLVCSVTLLITVLCSTLILLAVF
          KC.AQSEVAAPCSLKSEEICQWKNMQYKSILKN.LTVQVPVGLTIHTSLVCSVTLL.TVLCSTLILLAVF
Retrocopy KC*AQSEVAAPCSLKSEEICQWKNMQYKSILKN<LTVQVPVGLTIHTSLVCSVTLLTTVLCSTLILLAVF

Parental  KYGHFSL
          KYGHFSL
Retrocopy KYGHFSL

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.07 RPM	9.13 RPM
SRP017611_kidney	0.00 RPM	9.84 RPM
SRP017611_liver	0.00 RPM	5.98 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1998 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1998 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1998 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003759	1 retrocopy	retro_amel_386,
Callithrix jacchus	ENSCJAG00000013676	1 retrocopy	retro_cjac_2794,
Monodelphis domestica	ENSMODG00000018455	1 retrocopy	retro_mdom_1758,
Mustela putorius furo	ENSMPUG00000003841	1 retrocopy	retro_mputfur_1090,
Mus musculus	ENSMUSG00000023791	1 retrocopy	retro_mmus_943,
Oryctolagus cuniculus	ENSOCUG00000012329	1 retrocopy	retro_ocun_977,
Rattus norvegicus	ENSRNOG00000033623	2 retrocopies	retro_rnor_1998 , retro_rnor_2555,