RetrogeneDB ID: retro_rnor_2056

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:49554569..49554987(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Litaf
• Ensembl ID: ENSRNOG00000002520
• Aliases: Litaf, EET-1, Pig7
• Description: Lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog [Source:UniProtKB/Swiss-Prot;Acc:P0C0T0]

Sequence

>retro_rnor_2056
GTAATGCCCACCGCACCCCTCAACCTACGAAGAAACAGCGGTATCAACAGTTACTACCCAACGCCCCCAGCACCTATGCG
GAGGGACCAGCCACAGGGCTCATTACAGGCCCAAATGGGAAGGGCACGAATCTACCTTCGCACTAAAGCAGTCAGTGCCT
GTCCCCAACGCCAACGCAATTGCAGTGCAGACCGTTCATATGCAGCAGCCCGTCTCCTTCTATGACCGCCCTGTCCAGAT
GTGCTGTCCTTCCTGCAGCAAGACGATCATGACCCAACTGTCCTACAATGCCGGAGCCCTCACCTGACTCTCCTGTGGCA
GTCTGTGTCTGACGGGATGCATCACTGCCTGCTGCTTCATCCCATTCGGCGCAGACACCCTGCAGGATGTGGACCATTAC
TGCCCCAACTGCAGAGCA

Alignment

ORF - retro_rnor_2056 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.31 %
• Parental protein coverage: 86.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VMPTAP-PTYEETV-GVNSYY-PTPPAPQP-GPATGLITGPDGKGMNPPSY-YTQPVPVPNANAIAVQTV
          VMPTAP..TYEET..G.NSYY.P..P.....GPATGLITGP.GKG.N.PS....Q.VPVPNANAIAVQTV
Retrocopy VMPTAP>STYEETA<GINSYY<PNAPSTYAEGPATGLITGPNGKGTNLPSH<LKQSVPVPNANAIAVQTV

Parental  YVQQPISFYDRPIQMCCPSCNKMIVTQLSYNAGALTWLSCGSLCLLGCVAGCCFIPFCVDALQDVDHYCP
          ..QQP.SFYDRP.QMCCPSC.K.I.TQLSYNAGALT.LSCGSLCL.GC...CCFIPF..D.LQDVDHYCP
Retrocopy HMQQPVSFYDRPVQMCCPSCSKTIMTQLSYNAGALT*LSCGSLCLTGCITACCFIPFGADTLQDVDHYCP

Parental  NCKA
          NC.A
Retrocopy NCRA

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	0.22 RPM	22.79 RPM
SRP017611_kidney	0.00 RPM	95.25 RPM
SRP017611_liver	0.00 RPM	102.94 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2056 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2056 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2056 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006659	1 retrocopy	retro_cpor_704,
Macaca mulatta	ENSMMUG00000008784	1 retrocopy	retro_mmul_1411,
Monodelphis domestica	ENSMODG00000005014	4 retrocopies	retro_mdom_174, retro_mdom_574, retro_mdom_887, retro_mdom_911,
Otolemur garnettii	ENSOGAG00000028239	2 retrocopies	retro_ogar_1479, retro_ogar_2820,
Pteropus vampyrus	ENSPVAG00000009213	1 retrocopy	retro_pvam_261,
Rattus norvegicus	ENSRNOG00000002520	1 retrocopy	retro_rnor_2056 ,
Tupaia belangeri	ENSTBEG00000017097	1 retrocopy	retro_tbel_4388,
Tursiops truncatus	ENSTTRG00000010854	1 retrocopy	retro_ttru_1244,