RetrogeneDB ID: retro_rnor_595

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:101415575..101416001(-)
• Located in intron of: ENSRNOG00000037298

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lage3
• Ensembl ID: ENSRNOG00000037249
• Aliases: Lage3, RGD1562476
• Description: L antigen family member 3 [Source:RefSeq peptide;Acc:NP_001099815]

Sequence

>retro_rnor_595
GGCAATAATAACACTGCAGATGGCGCCAATGGTCTGACTGGCTGCTTCTGTCCTGGTAATGCAGGCACAATGGCAGTTAT
TCCCAGTGGAGCTCACCCTGTTGCAAGAGCACTGGAAGTCCCCCGAAATTCCAGCAAAAGCACCGTGCCTTTAACCCAAA
GGCCTGGAATCCGACATCATAGATTCGCCCTCTTCGTGCCCTTCCCGACCTCTTTGGAGGCAGAAATCGCCTGTGGGTCC
CTAGCTCCTGATGTTGAACCACACCAAGGACTGATAGGGAAGGAACTTAAAGTGAGCGGCAGCGTCCTGGAGGTGCACTG
GACCTCGGAAGATTCTCGCCTCCTCCGAATTTCCATCATGAACTTTCTTGACCAGCTTTCCCTAGTGGTGAACACCGTTC
AGGTCTTTGGGCCCCCGTTTTCCTGT

Alignment

ORF - retro_rnor_595 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.62 %
• Parental protein coverage: 95.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLSHTAGGADSPTGRFCPGNAGTMAVLPSGAHPVARALEAPRNSSKSSVPLTQRPGIRHHKFALFVPFPT
          G...TA.GA...TG.FCPGNAGTMAV.PSGAHPVARALE.PRNSSKS.VPLTQRPGIRHH.FALFVPFPT
Retrocopy GNNNTADGANGLTGCFCPGNAGTMAVIPSGAHPVARALEVPRNSSKSTVPLTQRPGIRHHRFALFVPFPT

Parental  SLEAEIACGSLAPDVEPHQGLVEKELKVSGSVLEVHWIAEDSRLLRISIMNFLDQLSLVVNTIQLFGPPI
          SLEAEIACGSLAPDVEPHQGL..KELKVSGSVLEVHW..EDSRLLRISIMNFLDQLSLVVNT.Q.FGPP.
Retrocopy SLEAEIACGSLAPDVEPHQGLIGKELKVSGSVLEVHWTSEDSRLLRISIMNFLDQLSLVVNTVQVFGPPF

Parental  SC
          SC
Retrocopy SC

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	1.51 RPM	27.61 RPM
SRP017611_kidney	0.14 RPM	32.66 RPM
SRP017611_liver	0.00 RPM	17.62 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_595 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_595 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_595 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024143	1 retrocopy	retro_dnov_244,
Dipodomys ordii	ENSDORG00000009093	1 retrocopy	retro_dord_448,
Homo sapiens	ENSG00000196976	1 retrocopy	retro_hsap_4244,
Gorilla gorilla	ENSGGOG00000013507	1 retrocopy	retro_ggor_2845,
Macaca mulatta	ENSMMUG00000007739	1 retrocopy	retro_mmul_1145,
Mus musculus	ENSMUSG00000015289	2 retrocopies	retro_mmus_1411, retro_mmus_1665,
Nomascus leucogenys	ENSNLEG00000014285	1 retrocopy	retro_nleu_1373,
Ochotona princeps	ENSOPRG00000003778	2 retrocopies	retro_opri_196, retro_opri_549,
Pongo abelii	ENSPPYG00000020881	1 retrocopy	retro_pabe_3394,
Rattus norvegicus	ENSRNOG00000037249	1 retrocopy	retro_rnor_595 ,
Sus scrofa	ENSSSCG00000025528	1 retrocopy	retro_sscr_94,