RetrogeneDB ID: retro_rnor_2397

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:123609101..123609844(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Lsm14a
• Ensembl ID: ENSRNOG00000021133
• Aliases: Lsm14a, RGD1305695
• Description: protein LSM14 homolog A [Source:RefSeq peptide;Acc:NP_001121024]

Sequence

>retro_rnor_2397
AGCCAGAACACCCCTTACATTGGTAACAAGATCAGCCTCTTTTCCCAGGTGGAGATCTGCTCTGAGGGCATCTTCTACAC
CATCGACACTGAGAACTCCACCGTAGCCTTTGTCAAAGTTTGATCCTTCAGTAGAACAGACATACCAACAGATCATCCAA
AACTGCCTCCAGATAAAGTCTTTGAATATATGATATTCCACGGGAGTGACATTAAAGACCCCACTTGTCTGTAGCCACTG
AAACCTCAATGTTCTTTGCCTCAGGACCCAGCTATTGCTCAGTCTTCATTAGATTCGTCTTCTTCATTCCGGTCAGTGGG
TTACTACGGACCTTTCGGGAGGATGCTCGTATATAATCAGTTCAGTATAAGTGCATTAGTTGGGCAGCAGCAGTTGGATG
CTGTTGGTGTTGCTGGGAGCTCCTTAGCGTCCTTGGAACAGAAGCGTCAAGTAGTGGTACCTTATCCCCGAGCAGTGCAG
TCGGTTCTGCCTTCACACAAGACACAAGATCTGTAAAACCACAGCTAGCCCGAGATCGATCAAGCCCTCAGTTAGACCCT
TTGAGAAAAAGTTCAACCACGGTACAAGCAGCATCTACTGCCTTGGCCCACTTACCTGGTCCAGCATCTGTTGGGAGAAG
GAGCCCCGTTCTAGCCAGGCCTTTGCCAGACAGCCAGAAAGCAACAGACGGCCAAGAGCACAGGGAAGCTGGAGTATACA
AAGTCCCAAGGCCAGAGCAGAAA

Alignment

ORF - retro_rnor_2397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.31 %
• Parental protein coverage: 53.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGSD
          S..TPYIG.KISL.S..EI..EGI.YTIDTENSTVA..KV.SF...D.PTD.P..P.D.VFEY.IF.GSD
Retrocopy SQNTPYIGNKISLFSQVEICSEGIFYTIDTENSTVAFVKV*SFSRTDIPTDHPKLPPDKVFEYMIFHGSD

Parental  IKDLTVCEPPKPQCSLPQDPAIVQSSLGSSSSSFQSVGSYGPFGRMPAYSQFSPSTLVG-QQFGAVGVAG
          IKD.T...P.KPQCSLPQDPAI.QSSL..SSSSF.SVG.YGPFGRM..Y.QFS.S.LVG.QQ..AVGVAG
Retrocopy IKDPTCL*PLKPQCSLPQDPAIAQSSL-DSSSSFRSVGYYGPFGRMLVYNQFSISALVGQQQLDAVGVAG

Parental  SSLTS-FGTEASNSGTLSQSNAVGSAFTQDTRSVKPQLAQGRSSPQLDPLRKSPTMEQAVQTASAHLPAP
          SSL.S..GTEAS.SGTLS.S.AVGSAFTQDTRSVKPQLA..RSSPQLDPLRKS.T..QA..TA.AHLP.P
Retrocopy SSLAS<LGTEASSSGTLSPSSAVGSAFTQDTRSVKPQLARDRSSPQLDPLRKSSTTVQAASTALAHLPGP

Parental  APVGRRSPVPARPLPPTSQKAIDNQEHRRAEVHKVPRPENE
          A.VGRRSPV.ARPL.P.SQKA.D.QEHR.A.V.KVPRPE..
Retrocopy ASVGRRSPVLARPL-PDSQKATDGQEHREAGVYKVPRPEQK

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	45.22 RPM
SRP017611_kidney	0.00 RPM	67.55 RPM
SRP017611_liver	0.00 RPM	33.35 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2397 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2397 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2397 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006555	1 retrocopy	retro_chof_1375,
Callithrix jacchus	ENSCJAG00000010360	5 retrocopies	retro_cjac_1582, retro_cjac_2625, retro_cjac_3201, retro_cjac_3327, retro_cjac_840,
Gorilla gorilla	ENSGGOG00000001762	1 retrocopy	retro_ggor_2378,
Microcebus murinus	ENSMICG00000011598	1 retrocopy	retro_mmur_1605,
Myotis lucifugus	ENSMLUG00000003368	1 retrocopy	retro_mluc_1793,
Macaca mulatta	ENSMMUG00000021614	2 retrocopies	retro_mmul_1386, retro_mmul_1860,
Nomascus leucogenys	ENSNLEG00000011713	4 retrocopies	retro_nleu_1299, retro_nleu_2544, retro_nleu_2580, retro_nleu_485,
Oryctolagus cuniculus	ENSOCUG00000011872	2 retrocopies	retro_ocun_193, retro_ocun_860,
Otolemur garnettii	ENSOGAG00000002492	2 retrocopies	retro_ogar_2586, retro_ogar_67,
Pongo abelii	ENSPPYG00000009832	2 retrocopies	retro_pabe_1693, retro_pabe_2906,
Pan troglodytes	ENSPTRG00000010813	3 retrocopies	retro_ptro_1343, retro_ptro_2389, retro_ptro_863,
Rattus norvegicus	ENSRNOG00000021133	1 retrocopy	retro_rnor_2397 ,
Ictidomys tridecemlineatus	ENSSTOG00000002785	1 retrocopy	retro_itri_170,