RetrogeneDB ID: retro_rnor_622

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:179704378..179704810(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000036784
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RGD1311703
• Ensembl ID: ENSRNOG00000020436
• Aliases: None
• Description: small acidic protein [Source:RefSeq peptide;Acc:NP_001013920]

Sequence

>retro_rnor_622
AAGAAAGAAAACTTCTTGAGACTTATGGGTACAGGAAAGAAAGAACACACTGGTTGTCTTGTTATAGGAGATCACAAATA
AACCTCTCACTTCAGAACAGGGGAAGAAGACAAGAAAATGAAGAGCTGGAGTCTCAGTACCAGCAGAGCATGGACAGCAA
ACTCTCAGGATCGTAGTGGGGCAGAACTGCGGCTCGATTTCAGCGAGGTAGAAGATCATGATGGAGAAAGTGATGTGGCT
GGAGATGATGATGAAGACGACCTTCCTGATGCAGTGAATCCAGATGACTCAGACAGCGATTCTAAGTCTGAGAAGGAGGA
GTCTTCAGAAGAGCTTCACGCTGCTGTGCATTCTGATGACACAGAAGACCCAAAGAGCAAAAAAGATGCGAAGAGCAATT
ATAAGATGATGTTTGTCAAGTCCAGTGGCTCA

Alignment

ORF - retro_rnor_622 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 80.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKQKFLRLMGAGKKEHTGRLVIGDHKSTSHFRTGEEDKKI-NEELESQYQQSMDSKLSG-RYRRHCGLGF
          .K..FLRLMG.GKKEHTG.LVIGDHK.TSHFRTG.E..K..NEELESQYQQSMDSKLSG.R......L.F
Retrocopy KKENFLRLMGTGKKEHTGCLVIGDHK*TSHFRTG-EEDKK<NEELESQYQQSMDSKLSG>RSGAELRLDF

Parental  SEVEDHDGEGDVAGDDDEDDSPDAESPDDSDSDSESEKEESAEELHAAAHPDDTEDPKSKKDAKSSYKMM
          SEVEDHDGE.DVAGDDDEDD.PDA..PDDSDSDS.SEKEES.EELHAA.H.DDTEDPKSKKDAKS.YKMM
Retrocopy SEVEDHDGESDVAGDDDEDDLPDAVNPDDSDSDSKSEKEESSEELHAAVHSDDTEDPKSKKDAKSNYKMM

Parental  FVKSSGS
          FVKSSGS
Retrocopy FVKSSGS

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	0.00 RPM	56.58 RPM
SRP017611_kidney	0.00 RPM	47.10 RPM
SRP017611_liver	0.00 RPM	20.17 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_622 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_622 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_622 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030220	2 retrocopies	retro_cfam_160, retro_cfam_717,
Callithrix jacchus	ENSCJAG00000009626	1 retrocopy	retro_cjac_3098,
Cavia porcellus	ENSCPOG00000009679	2 retrocopies	retro_cpor_1331, retro_cpor_772,
Equus caballus	ENSECAG00000011778	1 retrocopy	retro_ecab_269,
Felis catus	ENSFCAG00000027747	1 retrocopy	retro_fcat_2016,
Homo sapiens	ENSG00000110696	2 retrocopies	retro_hsap_1408, retro_hsap_3898,
Macropus eugenii	ENSMEUG00000011795	1 retrocopy	retro_meug_1432,
Myotis lucifugus	ENSMLUG00000001589	1 retrocopy	retro_mluc_2604,
Monodelphis domestica	ENSMODG00000007147	2 retrocopies	retro_mdom_1249, retro_mdom_672,
Mus musculus	ENSMUSG00000030663	2 retrocopies	retro_mmus_2190, retro_mmus_2616,
Nomascus leucogenys	ENSNLEG00000017719	1 retrocopy	retro_nleu_1425,
Otolemur garnettii	ENSOGAG00000025335	2 retrocopies	retro_ogar_1613, retro_ogar_2569,
Ochotona princeps	ENSOPRG00000000154	1 retrocopy	retro_opri_761,
Pongo abelii	ENSPPYG00000003458	2 retrocopies	retro_pabe_1166, retro_pabe_3178,
Rattus norvegicus	ENSRNOG00000020436	1 retrocopy	retro_rnor_622 ,