RetrogeneDB ID: retro_rnor_1485

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:43013618..43014243(+)
• Located in intron of: ENSRNOG00000011032

Retrocopy information

• Ensembl ID: ENSRNOG00000050458
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Snurf
• Ensembl ID: ENSRNOG00000015976
• Aliases: Snrpn, FE 294, FE 294 psi, FE294, FE294 psi
• Description: Small nuclear ribonucleoprotein-associated protein N [Source:UniProtKB/Swiss-Prot;Acc:P63164]

Sequence

>retro_rnor_1485
TATAGAATGAGATATATTCTGCAAGATGGAAGACTCTTCATTTGGTGCCTTTAAGGCTTTTGACAGGTGTATGAATTTGA
TCCTCTGTGATTGTGATGAGTTCAGGAAGATCAAGCCAGAGAATGCAAAACAACCAGAATGTGAAGAAAAACAGGTTTTG
GGTCTGGTCTTGCTACGTGGGGAGAACTTGGTTTCCATGACTGTGGAGGGTTCACCTCCTAAGGATACTGGCATTGCTCG
TGTGACACTTGCTGGTGCTGCAGGTGGCCCTGGGGTTGGAAGAGCAGCTGGCAGAAGAGTACCAGCATGTGTACCTATTC
CCCAAGCTGCTGCTGGATTAGCAGGCCCTGTCCAAGGAGTTAGAGGCCCACACCAGCAGGTCATGACCCCACAGGGAAGA
GGCACTGTTGCACCTGCTGCTGCTGCTGCTACTAGTAGTATTGCAGGAGCTCCAGCCCAGTACCCGCCAGGACAGGGACC
TCCACCTCCACCTGTAGGCAGAGCGACCCCATCTCCAGGCATTATGGCTCCTCTGCCTGGTATGAGACCACCCATGGGCC
CACCAATTGGCCTTTCCCCTGCTCAAGGGACACCTATAGGCATGCCCCCTCCAGGAATGAGACCC

Alignment

ORF - retro_rnor_1485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.08 %
• Parental protein coverage: 86.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YRMRCILQDGRIFI-GTFKAFDKHMNLILCDCDEFRKIKPKNAKQPEREEKRVLGLVLLRGENLVSMTVE
          YRMR.ILQDGR.FI.G.FKAFD..MNLILCDCDEFRKIKP.NAKQPE.EEK.VLGLVLLRGENLVSMTVE
Retrocopy YRMRYILQDGRLFI>GAFKAFDRCMNLILCDCDEFRKIKPENAKQPECEEKQVLGLVLLRGENLVSMTVE

Parental  GPPPKDTGIARVPLAGAAGGPGVGRAAGRGVPAGVPIPQAPAGLAGPVRGVGGPSQQVMTPQGRGTVAAA
          G.PPKDTGIARV.LAGAAGGPGVGRAAGR.VPA.VPIPQA.AGLAGPV.GV.GP.QQVMTPQGRGTVA.A
Retrocopy GSPPKDTGIARVTLAGAAGGPGVGRAAGRRVPACVPIPQAAAGLAGPVQGVRGPHQQVMTPQGRGTVAPA

Parental  AVAATASIAGAPTQYPPGRGTPPPPVGRATPPPGIMAPPPGMRPPMGPPIGLPPARGTPIGMPPPGMRP
          A.AAT.SIAGAP.QYPPG.G.PPPPVGRATP.PGIMAP.PGMRPPMGPPIGL.PA.GTPIGMPPPGMRP
Retrocopy AAAATSSIAGAPAQYPPGQGPPPPPVGRATPSPGIMAPLPGMRPPMGPPIGLSPAQGTPIGMPPPGMRP

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	448.27 RPM
SRP017611_kidney	0.00 RPM	13.82 RPM
SRP017611_liver	0.13 RPM	1.28 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1485 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1485 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1485 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007034	3 retrocopies	retro_amel_1048, retro_amel_714, retro_amel_839,
Bos taurus	ENSBTAG00000008251	1 retrocopy	retro_btau_620,
Canis familiaris	ENSCAFG00000010127	6 retrocopies	retro_cfam_1753, retro_cfam_1874, retro_cfam_2039, retro_cfam_627, retro_cfam_682, retro_cfam_752,
Choloepus hoffmanni	ENSCHOG00000001846	2 retrocopies	retro_chof_2275, retro_chof_385,
Cavia porcellus	ENSCPOG00000020270	1 retrocopy	retro_cpor_878,
Felis catus	ENSFCAG00000022298	2 retrocopies	retro_fcat_1390, retro_fcat_1895,
Homo sapiens	ENSG00000128739	1 retrocopy	retro_hsap_2580,
Gorilla gorilla	ENSGGOG00000003988	1 retrocopy	retro_ggor_1615,
Loxodonta africana	ENSLAFG00000009458	1 retrocopy	retro_lafr_1012,
Myotis lucifugus	ENSMLUG00000023361	3 retrocopies	retro_mluc_1192, retro_mluc_1816, retro_mluc_2156,
Macaca mulatta	ENSMMUG00000023139	1 retrocopy	retro_mmul_644,
Mustela putorius furo	ENSMPUG00000014638	1 retrocopy	retro_mputfur_1080,
Mus musculus	ENSMUSG00000000948	3 retrocopies	retro_mmus_1285, retro_mmus_1733, retro_mmus_665,
Oryctolagus cuniculus	ENSOCUG00000003532	4 retrocopies	retro_ocun_1291, retro_ocun_488, retro_ocun_689, retro_ocun_846,
Otolemur garnettii	ENSOGAG00000007392	5 retrocopies	retro_ogar_1179, retro_ogar_3042, retro_ogar_3060, retro_ogar_475, retro_ogar_722,
Pongo abelii	ENSPPYG00000006269	1 retrocopy	retro_pabe_1900,
Pan troglodytes	ENSPTRG00000006826	1 retrocopy	retro_ptro_1507,
Rattus norvegicus	ENSRNOG00000006961	2 retrocopies	retro_rnor_2825, retro_rnor_474,
Rattus norvegicus	ENSRNOG00000015976	6 retrocopies	retro_rnor_1122, retro_rnor_1314, retro_rnor_1485 , retro_rnor_2161, retro_rnor_2462, retro_rnor_2517,
Sus scrofa	ENSSSCG00000028124	2 retrocopies	retro_sscr_350, retro_sscr_405,
Ictidomys tridecemlineatus	ENSSTOG00000001339	1 retrocopy	retro_itri_44,
Tursiops truncatus	ENSTTRG00000010966	5 retrocopies	retro_ttru_1005, retro_ttru_1051, retro_ttru_1473, retro_ttru_580, retro_ttru_600,