RetrogeneDB ID: retro_rnor_1780

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:22770197..22770760(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fbl
• Ensembl ID: ENSRNOG00000019229
• Aliases: None
• Description: rRNA 2'-O-methyltransferase fibrillarin [Source:UniProtKB/Swiss-Prot;Acc:P22509]

Sequence

>retro_rnor_1780
GAAGGAGATGACAAAATTGAGTACCGAGCCTAGAAACCCTTCTGTTCAAAGCTGACTGCAGTAATCCTGGGCCCATAGAA
CAGATCCACATCAAGCCTGTGGCCAAGGTGCTCTACCTTGGGGCAGCCTCAGGCACCACCTTCTCCCATGTCTCTGATAC
CGTCTGCCCAGATGGTCGGGTCTATGCAGTTGAGTTCTCCCACGGATCTGGCCGTGACCTCATCAACTTGGCAAAGAAGA
GGACCAACATTATTCCTGCAATTGAAGATGCTCAGCACGCACACAAATACTGCATGCTTATTGCAATGGTGGATGTCATA
TTTGCCGATGTGGCCCAGCCAGACCAAACCCGAATTGTGGCCCGGAATCTCCACACCTTCCTACAGAATGGAGGGCATTT
TGTGATTTGCATTAAGGCCAACTGCATTGACTCCACAGAAGCTGTGGTTGCATCTGAAGTGAAAATGATGCAGCAAGAGA
ACATGAAGCCCCAGGAGTATTTCATGCTAGCGCCTTATGAAAGCGACCACGCTGTGTGCAGGCCACCTCCCAAGGGAAAG
AAC

Alignment

ORF - retro_rnor_1780 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.1 %
• Parental protein coverage: 59.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EGDDKIEYRAWNPFRSKLAAAILGG-VDQIHIKPGAKVLYLGAASGTTVSHVSDIVGPDGLVYAVEFSHR
          EGDDKIEYRA..PF.SKL.A.ILG....QIHIKP.AKVLYLGAASGTT.SHVSD.V.PDG.VYAVEFSH.
Retrocopy EGDDKIEYRA*KPFCSKLTAVILGP<IEQIHIKPVAKVLYLGAASGTTFSHVSDTVCPDGRVYAVEFSHG

Parental  SGRDLINLAKKRTNIIPVIEDARHPHKYRMLIAMVDVIFADVAQPDQTRIVALNAHTFLRNGGHFVISIK
          SGRDLINLAKKRTNIIP.IEDA.H.HKY.MLIAMVDVIFADVAQPDQTRIVA.N.HTFL.NGGHFVI.IK
Retrocopy SGRDLINLAKKRTNIIPAIEDAQHAHKYCMLIAMVDVIFADVAQPDQTRIVARNLHTFLQNGGHFVICIK

Parental  ANCIDSTASAEAVFASEVKKMQQENMKPQEQLTLEPYERDHAVVVGVYRPPPKAKN
          ANCIDST...EAV.ASEVK.MQQENMKPQE...L.PYE.DHAV.....RPPPK.KN
Retrocopy ANCIDST---EAVVASEVKMMQQENMKPQEYFMLAPYESDHAVC----RPPPKGKN

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	17.33 RPM
SRP017611_kidney	0.00 RPM	19.68 RPM
SRP017611_liver	0.00 RPM	9.55 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1780 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1780 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1780 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002579	1 retrocopy	retro_btau_108,
Canis familiaris	ENSCAFG00000005412	1 retrocopy	retro_cfam_1697,
Equus caballus	ENSECAG00000023221	1 retrocopy	retro_ecab_308,
Homo sapiens	ENSG00000105202	1 retrocopy	retro_hsap_99,
Loxodonta africana	ENSLAFG00000000171	1 retrocopy	retro_lafr_23,
Macropus eugenii	ENSMEUG00000014684	1 retrocopy	retro_meug_1077,
Microcebus murinus	ENSMICG00000007686	1 retrocopy	retro_mmur_1127,
Mus musculus	ENSMUSG00000046865	4 retrocopies	retro_mmus_1141, retro_mmus_1585, retro_mmus_1609, retro_mmus_89,
Nomascus leucogenys	ENSNLEG00000014234	1 retrocopy	retro_nleu_1947,
Otolemur garnettii	ENSOGAG00000006463	2 retrocopies	retro_ogar_3102, retro_ogar_504,
Pan troglodytes	ENSPTRG00000010982	2 retrocopies	retro_ptro_2208, retro_ptro_3074,
Pteropus vampyrus	ENSPVAG00000010849	1 retrocopy	retro_pvam_231,
Rattus norvegicus	ENSRNOG00000019229	4 retrocopies	retro_rnor_1082, retro_rnor_1780 , retro_rnor_643, retro_rnor_75,
Sorex araneus	ENSSARG00000008709	1 retrocopy	retro_sara_768,
Sus scrofa	ENSSSCG00000030510	1 retrocopy	retro_sscr_39,
Ictidomys tridecemlineatus	ENSSTOG00000012486	1 retrocopy	retro_itri_1302,
Tupaia belangeri	ENSTBEG00000007755	2 retrocopies	retro_tbel_3774, retro_tbel_3974,
Tursiops truncatus	ENSTTRG00000003967	1 retrocopy	retro_ttru_30,