RetrogeneDB ID: retro_rnor_56

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:115773839..115774556(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000011827
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Psmb6
• Ensembl ID: ENSRNOG00000019551
• Aliases: Psmb6, Psmb6l
• Description: Proteasome subunit beta type-6 [Source:UniProtKB/Swiss-Prot;Acc:P28073]

Sequence

>retro_rnor_56
ATGGCGGCCGCCTTAGCTGTTCGTGGAGCCATCTCTGCACCGGCCTTTGGGCCGGAGGCGCTCACTCCAGACTGGGAAAA
CCGAGAAGTCTCCACAGGGACCACGATCATGGCTGTGCAATTTGACGGGGGCGTGGTTCTAGGAGCAGACTCCAGAACAA
CCACTGGGTCGTACATCGCCAATCGAGTGACTGACAAGCTGACCCCTATCCACGATCACATCTTCTGCTGCCGCTCAGGC
TCGGCAGCTGATACCCAAGCAGTAGCTGATGCTGTCACGTACCAGCTTGGTTTCCACAGTATTGAGCTGAACGAGCCTCC
ACTAGTGCACACAGCCGCCAGTCTCTTTAAGGAGATGTGTTACCGCTACAGAGAAGATCTGATGGCAGGAATCATCATCG
CAGGCTGGGACCCTCAAGAAGGAGGGCAGGTGTACTCTGTTCCCATGGGAGGTATGATGGTAAGACAGTCCTTTGCCATC
GGAGGCTCCGGGAGCTCATATATCTATGGCTATGTTGATGCTACCTATCGGGAAGGCATGACCAAGGATGAATGTCTGCA
ATTCACTGCCAATGCTCTTGCTTTGGCTATGGAACGGGATGGCTCCAGTGGAGGAGTGATCCGCTTGGCAGCCATTCAAC
AGTCGGGGGTAGAGCGGCAGGTGCTTTTGGGAGACCAGATCCCCAAGGTCACCATCTCCACTTTGCCACCTCCCTGA

Alignment

ORF - retro_rnor_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.58 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAALAVRGAVSAPAFGPEALTPDWENREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPI
          MAAALAVRGA.SAPAFGPEALTPDWENREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPI
Retrocopy MAAALAVRGAISAPAFGPEALTPDWENREVSTGTTIMAVQFDGGVVLGADSRTTTGSYIANRVTDKLTPI

Parental  HDHIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGWDPQE
          HDHIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGWDPQE
Retrocopy HDHIFCCRSGSAADTQAVADAVTYQLGFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGWDPQE

Parental  GGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKDECLQFTANALALAMERDGSSGGVIRLA
          GGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKDECLQFTANALALAMERDGSSGGVIRLA
Retrocopy GGQVYSVPMGGMMVRQSFAIGGSGSSYIYGYVDATYREGMTKDECLQFTANALALAMERDGSSGGVIRLA

Parental  AIQQSGVERQVLLGDQIPKVTISTLPPP
          AIQQSGVERQVLLGDQIPKVTISTLPPP
Retrocopy AIQQSGVERQVLLGDQIPKVTISTLPPP

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	0.29 RPM	24.66 RPM
SRP017611_kidney	0.14 RPM	25.40 RPM
SRP017611_liver	0.00 RPM	19.90 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_56 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_56 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_56 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016075	1 retrocopy	retro_amel_1834,
Bos taurus	ENSBTAG00000013390	2 retrocopies	retro_btau_1734, retro_btau_534,
Canis familiaris	ENSCAFG00000015855	1 retrocopy	retro_cfam_2173,
Callithrix jacchus	ENSCJAG00000012010	1 retrocopy	retro_cjac_775,
Dipodomys ordii	ENSDORG00000005851	1 retrocopy	retro_dord_613,
Erinaceus europaeus	ENSEEUG00000002083	3 retrocopies	retro_eeur_203, retro_eeur_607, retro_eeur_71,
Felis catus	ENSFCAG00000008036	2 retrocopies	retro_fcat_1813, retro_fcat_1995,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Microcebus murinus	ENSMICG00000014854	2 retrocopies	retro_mmur_140, retro_mmur_718,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Mus musculus	ENSMUSG00000018286	2 retrocopies	retro_mmus_348, retro_mmus_3569,
Otolemur garnettii	ENSOGAG00000009653	1 retrocopy	retro_ogar_2114,
Pteropus vampyrus	ENSPVAG00000006048	1 retrocopy	retro_pvam_618,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56 ,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689,
Ictidomys tridecemlineatus	ENSSTOG00000014871	1 retrocopy	retro_itri_514,
Tarsius syrichta	ENSTSYG00000010674	1 retrocopy	retro_tsyr_1807,
Tursiops truncatus	ENSTTRG00000000566	1 retrocopy	retro_ttru_405,
Vicugna pacos	ENSVPAG00000000595	1 retrocopy	retro_vpac_400,