RetrogeneDB ID: retro_rnor_1599

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:3668712..3669278(-)
• Located in intron of: ENSRNOG00000013282

Retrocopy information

• Ensembl ID: ENSRNOG00000040283
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Smarce1
• Ensembl ID: ENSRNOG00000010676
• Aliases: Smarce1, BAF57, RGD1304726
• Description: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 [Source:RefSeq peptide;Acc:NP_001020164]

Sequence

>retro_rnor_1599
CCGGGCACCAACAGCCGGGTCACCGCGTCCTCTGGCATTACAATTCCAAAGCCTCCAAAGCCACCAGATAAGCCGCTGAT
GGCCTACATGAGATACAGCAGAAAGGTCTGGAACCAATGAAAGGCTTCCAACCCTGACCTAAAGTTGTGGGAGATTGGCA
CAATTATTGGTGGCATGTGGCAAGATCTCACTGATGAAGAGAAACAAGAATATTTAAATGAATACGAAGCAGAAAAGATA
GAGCACAATGAATCTATGAAGGCCTATCATAATTCCCCGCATACCTTGCGTATATTAATGCAAAAAGCCGTGCAGAAGTT
GCATTAGAGGAAGAAAGTCAACAGACACAGTTGCACGTGGAGAAAGAACCTTACATGAGCATTCAGCCTGCTGAGGATCT
AGACGATTATGATGATGGCTTTTCAATGAAGCATACAGCCACTGCCCATTTCCAGAGAAACCACAGCTTCATCAGTGAGT
TCCTCAGTGAGAGTGTGGTGCCTGATGTGCGGTCGGTTGTCACAACAGCTAGAATGCAGGTCCTCAAGCGACAGGTCCAG
TCTTTA

Alignment

ORF - retro_rnor_1599 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.43 %
• Parental protein coverage: 50.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PPTPAPATASSGITIPKPPKPPDKPLMPYMRYSRKVWDQVKASNPDLKLWEIGKIIGGMWRDLTDEEKQE
          P.T....TASSGITIPKPPKPPDKPLM.YMRYSRKVW.Q.KASNPDLKLWEIG.IIGGMW.DLTDEEKQE
Retrocopy PGTNSRVTASSGITIPKPPKPPDKPLMAYMRYSRKVWNQ*KASNPDLKLWEIGTIIGGMWQDLTDEEKQE

Parental  YLNEYEAEKIEYNESMKAYHNS-PAYLAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQPAEDPDDYD
          YLNEYEAEKIE.NESMKAYHNS.PAYLAYINAKSRAE.ALEEES.Q.Q...EK.EPYMSIQPAED.DDYD
Retrocopy YLNEYEAEKIEHNESMKAYHNS<PAYLAYINAKSRAEVALEEESQQTQLHVEK-EPYMSIQPAEDLDDYD

Parental  DGFSMKHTATARFQRNHRLISEILSESVVPDVRSVVTTARMQVLKRQVQSL
          DGFSMKHTATA.FQRNH..ISE.LSESVVPDVRSVVTTARMQVLKRQVQSL
Retrocopy DGFSMKHTATAHFQRNHSFISEFLSESVVPDVRSVVTTARMQVLKRQVQSL

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	33.29 RPM
SRP017611_kidney	0.00 RPM	37.26 RPM
SRP017611_liver	0.00 RPM	18.76 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1599 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1599 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1599 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016025	8 retrocopies	retro_cfam_1057, retro_cfam_1131, retro_cfam_1134, retro_cfam_1300, retro_cfam_1412, retro_cfam_1803, retro_cfam_2063, retro_cfam_2127,
Choloepus hoffmanni	ENSCHOG00000008727	3 retrocopies	retro_chof_1245, retro_chof_482, retro_chof_573,
Callithrix jacchus	ENSCJAG00000013573	4 retrocopies	retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Felis catus	ENSFCAG00000009646	2 retrocopies	retro_fcat_234, retro_fcat_513,
Homo sapiens	ENSG00000073584	5 retrocopies	retro_hsap_1195, retro_hsap_1304, retro_hsap_3623, retro_hsap_3947, retro_hsap_922,
Gorilla gorilla	ENSGGOG00000011803	2 retrocopies	retro_ggor_1020, retro_ggor_931,
Microcebus murinus	ENSMICG00000009821	4 retrocopies	retro_mmur_1408, retro_mmur_1592, retro_mmur_608, retro_mmur_928,
Myotis lucifugus	ENSMLUG00000004609	1 retrocopy	retro_mluc_1209,
Macaca mulatta	ENSMMUG00000004005	3 retrocopies	retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furo	ENSMPUG00000014660	4 retrocopies	retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Mus musculus	ENSMUSG00000037935	5 retrocopies	retro_mmus_1111, retro_mmus_1127, retro_mmus_2437, retro_mmus_2618, retro_mmus_3194,
Nomascus leucogenys	ENSNLEG00000001957	4 retrocopies	retro_nleu_1060, retro_nleu_2051, retro_nleu_2083, retro_nleu_286,
Oryctolagus cuniculus	ENSOCUG00000008981	1 retrocopy	retro_ocun_59,
Otolemur garnettii	ENSOGAG00000001652	7 retrocopies	retro_ogar_1734, retro_ogar_2059, retro_ogar_3199, retro_ogar_402, retro_ogar_454, retro_ogar_682, retro_ogar_760,
Ochotona princeps	ENSOPRG00000000985	1 retrocopy	retro_opri_731,
Pongo abelii	ENSPPYG00000008456	4 retrocopies	retro_pabe_2973, retro_pabe_3251, retro_pabe_794, retro_pabe_994,
Pan troglodytes	ENSPTRG00000022902	5 retrocopies	retro_ptro_2451, retro_ptro_2678, retro_ptro_3039, retro_ptro_639, retro_ptro_894,
Pteropus vampyrus	ENSPVAG00000011355	1 retrocopy	retro_pvam_237,
Rattus norvegicus	ENSRNOG00000010676	7 retrocopies	retro_rnor_1278, retro_rnor_1311, retro_rnor_1456, retro_rnor_1507, retro_rnor_1599 , retro_rnor_2383, retro_rnor_2593,
Tupaia belangeri	ENSTBEG00000000770	10 retrocopies	retro_tbel_1246, retro_tbel_1554, retro_tbel_2208, retro_tbel_2955, retro_tbel_4035, retro_tbel_4629, retro_tbel_4656, retro_tbel_658, retro_tbel_821, retro_tbel_844,
Tursiops truncatus	ENSTTRG00000013885	1 retrocopy	retro_ttru_1217,