RetrogeneDB ID: retro_rnor_2891

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:11730819..11731350(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000003789
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Fam133b
• Ensembl ID: ENSRNOG00000009163
• Aliases: Fam133b, RGD1306302
• Description: Protein FAM133B [Source:UniProtKB/Swiss-Prot;Acc:Q505I5]

Sequence

>retro_rnor_2891
ATGAGGAAGCGAGACAATCGCGTGGCCTACATGAATCCAATAGCAATGGCTCGGTCAAGGGGTCCAATCCAGTCTTCAGG
ACCAACAATCCAGGATTATCTGAATCGACCAAGGCCTACCTGGGAGGAAGTGAAGGAGCAGCTGGAAAAGAAAAAGAAGG
GCTCCAAGGCTTTGGCTGAGTTTGAAGAGAAAATGAATGAGAATTGGAAGAAAGAACTAGAAAAACATAGAGAAAAAGTA
TTAAGTGGAAATGAGAGCTCATCCAAAAAACGACAGAAAAAGAAAAAAGAAAAGAAGAAATCTGGTAGGTATTCATCTTC
TTCTTCATCGAGCTCTGATTCGTCCAGCAGTTCTTCAGATTCTGAGGATGAGGATAAAAAGCAAACAAAAAGAAGGAAGA
AAAAGAAGAGCCATTGCCATAAGTCTCGCGAGACCTCCGCGTCGGATTCAGACTCAGACAGCAAGGATGGTTCAAAAAAG
AAGTCAAGGGATGTAACTGAAAGAGAAAAAGCGAGTCAGCAAAAAGAGAAA

Alignment

ORF - retro_rnor_2891 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.16 %
• Parental protein coverage: 73.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGKRDNRVAYMNPIAMARSRGPIQSSGPTIQDYLNRPRPTWEEVKEQLEKKKKGSKALAEFEEKMNENWK
          M.KRDNRVAYMNPIAMARSRGPIQSSGPTIQDYLNRPRPTWEEVKEQLEKKKKGSKALAEF.........
Retrocopy MRKRDNRVAYMNPIAMARSRGPIQSSGPTIQDYLNRPRPTWEEVKEQLEKKKKGSKALAEFXXXXXXXXX

Parental  KELEKHREKLLSGNESSSKKRQKKKKEKKKSGRYSSSSSSSSDSSSSSSDSEEEDKKQTKRRKKKKSHCH
          ..........LSGNESSS............SGRYSSSSSSSSDSSSSSSDSE.ED............HCH
Retrocopy XXXXXXXXXXLSGNESSSXXXXXXXXXXXXSGRYSSSSSSSSDSSSSSSDSEDEDXXXXXXXXXXXXHCH

Parental  KSPETSVSDSDSDSKDGSKKKKKSKDITEREKDTKGLSK
          KS.ETS.SDSDSDSKDGS..KKKS.D.TEREK......K
Retrocopy KSRETSASDSDSDSKDGS--KKKSRDVTEREKASQQKEK

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	27.90 RPM
SRP017611_kidney	0.14 RPM	21.56 RPM
SRP017611_liver	0.00 RPM	10.62 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2891 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2891 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2891 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007438	1 retrocopy	retro_amel_102,
Callithrix jacchus	ENSCJAG00000013910	3 retrocopies	retro_cjac_1084, retro_cjac_1163, retro_cjac_4095,
Equus caballus	ENSECAG00000026810	1 retrocopy	retro_ecab_95,
Homo sapiens	ENSG00000234545	4 retrocopies	retro_hsap_2336, retro_hsap_3179, retro_hsap_55, retro_hsap_577,
Loxodonta africana	ENSLAFG00000029755	1 retrocopy	retro_lafr_594,
Myotis lucifugus	ENSMLUG00000005933	1 retrocopy	retro_mluc_2301,
Macaca mulatta	ENSMMUG00000019802	4 retrocopies	retro_mmul_1415, retro_mmul_226, retro_mmul_420, retro_mmul_765,
Mus musculus	ENSMUSG00000058503	2 retrocopies	retro_mmus_3481, retro_mmus_3519,
Nomascus leucogenys	ENSNLEG00000015333	1 retrocopy	retro_nleu_14,
Pongo abelii	ENSPPYG00000025825	1 retrocopy	retro_pabe_225,
Rattus norvegicus	ENSRNOG00000009163	1 retrocopy	retro_rnor_2891 ,
Sus scrofa	ENSSSCG00000015317	1 retrocopy	retro_sscr_49,
Ictidomys tridecemlineatus	ENSSTOG00000028195	1 retrocopy	retro_itri_12,
Tupaia belangeri	ENSTBEG00000011674	1 retrocopy	retro_tbel_1,