RetrogeneDB ID: retro_rnor_1960

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:37214441..37214865(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Psma6
• Ensembl ID: ENSRNOG00000007114
• Aliases: None
• Description: Proteasome subunit alpha type-6 [Source:UniProtKB/Swiss-Prot;Acc:P60901]

Sequence

>retro_rnor_1960
ATGTCCCATCATTCCAGCCCCAGTTTTGACCATCACATTACTATTTTCTCTCCCTCTGAAGGCTGACTCTACCAAGTAGA
ATATGCTTTTAAGGCTTTTAACTACCACAGAGGGCTTACATCTGTAGCTGTCAGAGGAAAAGGACTGCACAGTTATTGTC
ACACAGAAGAAAGTACCTGAGAAACAACTGGATTCCAGCACAGTGACTGACTTATTCAAGATAACAGAAAGTATTGGTTG
TGTGGTGACAGAAGTGACAGCTGACAGCTGATCCCAGATACAGAGGACACGCTATGAGGCAACTAAGTAGAAATAGAAAT
ATGGCTATGAGATTCCTGTGGACATGCTGTGTAAAAGAATTGCTGATATTTCTCAAACCTATACATAGAATGCTGAAATG
AGGTCACTTGGTTTCATCATTGTA

Alignment

ORF - retro_rnor_1960 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.06 %
• Parental protein coverage: 56.5 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSRGSSAGFDRHITIFSP-EGRLYQVEYAFKAIN-QGGLTSVAVRGK-DCAVIVTQKKVPDKLLDSSTVT
          MS..SS..FD.HITIFSP.EG.LYQVEYAFKA.N...GLTSVAVRGK.DC.VIVTQKKVP.K.LDSSTVT
Retrocopy MSHHSSPSFDHHITIFSPSEG*LYQVEYAFKAFNYHRGLTSVAVRGK>DCTVIVTQKKVPEKQLDSSTVT

Parental  HLFKITENIGCVMTGMTADSRSQVQRARYEAANWKYKYGYEIPVDMLCKRIADISQVYTQNAEMRPLGCC
          .LFKITE.IGCV.T..TADS.SQ.QR.RYEA...K.KYGYEIPVDMLCKRIADISQ.YT.NAEMR.LG..
Retrocopy DLFKITESIGCVVTEVTADS*SQIQRTRYEATK*K*KYGYEIPVDMLCKRIADISQTYT*NAEMRSLGFI

Parental  MI
          ..
Retrocopy IV

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	45.08 RPM
SRP017611_kidney	0.00 RPM	48.01 RPM
SRP017611_liver	0.00 RPM	44.04 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1960 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1960 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1960 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000013409	2 retrocopies	retro_cfam_1581, retro_cfam_743,
Echinops telfairi	ENSETEG00000004892	1 retrocopy	retro_etel_1775,
Felis catus	ENSFCAG00000026276	1 retrocopy	retro_fcat_973,
Homo sapiens	ENSG00000100902	2 retrocopies	retro_hsap_1228, retro_hsap_4923,
Macropus eugenii	ENSMEUG00000016537	1 retrocopy	retro_meug_1217,
Microcebus murinus	ENSMICG00000000083	4 retrocopies	retro_mmur_104, retro_mmur_165, retro_mmur_752, retro_mmur_80,
Myotis lucifugus	ENSMLUG00000010228	1 retrocopy	retro_mluc_822,
Macaca mulatta	ENSMMUG00000016544	1 retrocopy	retro_mmul_343,
Mustela putorius furo	ENSMPUG00000016288	1 retrocopy	retro_mputfur_1089,
Mus musculus	ENSMUSG00000021024	1 retrocopy	retro_mmus_654,
Otolemur garnettii	ENSOGAG00000008492	10 retrocopies	retro_ogar_1273, retro_ogar_1397, retro_ogar_1928, retro_ogar_1950, retro_ogar_2021, retro_ogar_2073, retro_ogar_2274, retro_ogar_2488, retro_ogar_2521, retro_ogar_3089,
Pan troglodytes	ENSPTRG00000006264	2 retrocopies	retro_ptro_3297, retro_ptro_844,
Rattus norvegicus	ENSRNOG00000007114	4 retrocopies	retro_rnor_1724, retro_rnor_1960 , retro_rnor_854, retro_rnor_924,
Ictidomys tridecemlineatus	ENSSTOG00000011774	1 retrocopy	retro_itri_1713,
Tupaia belangeri	ENSTBEG00000011241	17 retrocopies	retro_tbel_1304, retro_tbel_1415, retro_tbel_1789, retro_tbel_2028, retro_tbel_2466, retro_tbel_2519, retro_tbel_3227, retro_tbel_3280, retro_tbel_3535, retro_tbel_4181, retro_tbel_4183, retro_tbel_4357, retro_tbel_4465, retro_tbel_4495, retro_tbel_509, retro_tbel_602, retro_tbel_725,