RetrogeneDB ID: retro_rnor_2845

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:108014677..108015183(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lsm12
• Ensembl ID: ENSRNOG00000020894
• Aliases: Lsm12, RGD1309441
• Description: None

Sequence

>retro_rnor_2845
AAGTTGGTAGCTTTCGACTACCAGTCCAAAATGCTGGCTCTAAAATGTCCCTCCTCCAGCAGAAAGCCTAACCAGGCAGA
CATCTTGCTTATAAACTTACAGTATGTTTCAGAAGTGGAAATAATTAAAGATCGAACAGAAATCCCTCCTCTTCTAGCTT
CACTCAATGTTGGTAAGCTTGACAGCAAAGTACCAACAGAGGAGGAGGAGAAGCTGAGCCAGGCCTATGCAATCAGCGCT
AGGGTCTCCCTGGAGGGCCCGCAGCTCTTCCAGACCATTCACAAGATCATTAAAGACTGTAAATGGCAAGAAAAAAAACC
ATTGTAGTCGTGGAGGAAGTTGTTATTACACCCCCATATCAAGTGGAAAGTTGTAAAAGCAAAGAGGGGAGTGCACTGAG
CCATGTACGCAAAATAGTTGAAAAACAGTTCAGAGACCTGGAAAGTCAAAAGATACTGCAGCGTTCACAAGCCCAACAAC
CACAGAAGGAGTCTGCCCTGTCATCC

Alignment

ORF - retro_rnor_2845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 86.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EVVAFDYQSKMLALKCPSSSGKPNHADILLINLQYVSEVEIINDRTETPPPLASLNVSKLASKARTEKEE
          ..VAFDYQSKMLALKCPSSS.KPN.ADILLINLQYVSEVEII.DRTE.PP.LASLNV.KL.SK..TE.EE
Retrocopy KLVAFDYQSKMLALKCPSSSRKPNQADILLINLQYVSEVEIIKDRTEIPPLLASLNVGKLDSKVPTEEEE

Parental  KLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQ-EKNIVVMEEVV-ITPPYQVENCKGKEGSALSHVRKI
          KLSQAYAISA.VSLEG.QLFQTIHK.IKDCKWQ......V..E.V.ITPPYQVE.CK.KEGSALSHVRKI
Retrocopy KLSQAYAISARVSLEGPQLFQTIHKIIKDCKWQ<XXXXIVVVEEVVITPPYQVESCKSKEGSALSHVRKI

Parental  VEKHFRDVESQKILQRSQAQQPQKEAALSS
          VEK.FRD.ESQKILQRSQAQQPQKE.ALSS
Retrocopy VEKQFRDLESQKILQRSQAQQPQKESALSS

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	56.01 RPM
SRP017611_kidney	0.00 RPM	49.96 RPM
SRP017611_liver	0.00 RPM	28.24 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2845 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2845 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2845 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014379	2 retrocopies	retro_cfam_1843, retro_cfam_312,
Echinops telfairi	ENSETEG00000008374	1 retrocopy	retro_etel_21,
Felis catus	ENSFCAG00000029083	1 retrocopy	retro_fcat_787,
Homo sapiens	ENSG00000161654	1 retrocopy	retro_hsap_4041,
Loxodonta africana	ENSLAFG00000005202	1 retrocopy	retro_lafr_906,
Macropus eugenii	ENSMEUG00000007501	1 retrocopy	retro_meug_1462,
Macaca mulatta	ENSMMUG00000006804	1 retrocopy	retro_mmul_3,
Mus musculus	ENSMUSG00000020922	1 retrocopy	retro_mmus_2683,
Otolemur garnettii	ENSOGAG00000010489	2 retrocopies	retro_ogar_1771, retro_ogar_2447,
Oryzias latipes	ENSORLG00000011310	1 retrocopy	retro_olat_12,
Rattus norvegicus	ENSRNOG00000020894	1 retrocopy	retro_rnor_2845 ,
Tupaia belangeri	ENSTBEG00000012523	2 retrocopies	retro_tbel_3062, retro_tbel_60,
Vicugna pacos	ENSVPAG00000011145	1 retrocopy	retro_vpac_627,