RetrogeneDB ID: retro_rnor_1499

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:73625842..73626170(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Akirin2
• Ensembl ID: ENSRNOG00000008288
• Aliases: Akirin2, FBI1, RGD1307791
• Description: Akirin-2 [Source:UniProtKB/Swiss-Prot;Acc:Q25C79]

Sequence

>retro_rnor_1499
AGAAAACATTTGGAAACCCCTTCTCATCTTAAAGATCCAGGTTGTGGTTCTCAGGCATAGCCACAAGTATTTCTCCTCCA
TGGACCAGTTACACCAGTGACATGATGGGCAGCATCTTCCCCATCCATAGAAGAGCAGCCTTTATTTACTTTGTGGCAGA
ATAGAATAATCTGTAAATGTTTTGTAAAAAGAGAGTGAAGAGGAAGTTTGAGGAAAGTGTGAGGAAATAGTCCACATAAA
ATGAGCAGGACAATATGATGCACTTGTGAAGATTATACATGATCAAATAATGTCACAATATGGAGAAGAGCCTGCCAACT
GTGCTTCA

Alignment

ORF - retro_rnor_1499 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.82 %
• Parental protein coverage: 54.23 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRHLEASFQQTDPGCSSDSQPHAFLISGPASPGTSSATSSPLKKEQPLFTLRQVGMICERLL-KEREEKV
          R.HLE......DPGC.S...P..FL..GP..P.T..A.SSP...EQPLFTL.Q...IC.....KE.EE.V
Retrocopy RKHLETPSHLKDPGCGSQA*PQVFLLHGPVTPVT*WAASSPSIEEQPLFTLWQNRIICKCFV>KESEEEV

Parental  REEYEEILNTKLAEQYDAFVKFTHDQIMRRYGEQPASYVS
          ....EEI...K.A.QYDA.VK..HDQIM..YGE.PA...S
Retrocopy *GKCEEIVHIK*AGQYDALVKIIHDQIMSQYGEEPANCAS

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	47.74 RPM
SRP017611_kidney	0.00 RPM	35.73 RPM
SRP017611_liver	0.00 RPM	14.32 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1499 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1499 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1499 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003082	1 retrocopy	retro_cfam_1014,
Choloepus hoffmanni	ENSCHOG00000012160	1 retrocopy	retro_chof_413,
Callithrix jacchus	ENSCJAG00000000769	1 retrocopy	retro_cjac_2231,
Dasypus novemcinctus	ENSDNOG00000000549	1 retrocopy	retro_dnov_1788,
Homo sapiens	ENSG00000135334	1 retrocopy	retro_hsap_2991,
Gorilla gorilla	ENSGGOG00000002448	1 retrocopy	retro_ggor_2071,
Macaca mulatta	ENSMMUG00000002824	1 retrocopy	retro_mmul_1914,
Pongo abelii	ENSPPYG00000016831	1 retrocopy	retro_pabe_2477,
Pan troglodytes	ENSPTRG00000018409	1 retrocopy	retro_ptro_2023,
Rattus norvegicus	ENSRNOG00000008288	1 retrocopy	retro_rnor_1499 ,
Sorex araneus	ENSSARG00000006084	1 retrocopy	retro_sara_701,
Sarcophilus harrisii	ENSSHAG00000011555	2 retrocopies	retro_shar_363, retro_shar_579,
Sus scrofa	ENSSSCG00000004307	1 retrocopy	retro_sscr_897,