RetrogeneDB ID: retro_rnor_1962

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:40111361..40111842(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Plscr2
• Ensembl ID: ENSRNOG00000033412
• Aliases: None
• Description: phospholipid scramblase 2 [Source:RefSeq peptide;Acc:NP_001014116]

Sequence

>retro_rnor_1962
CAGGCTGGCTACACACTCACAACAGCTGGCTGTGGAACTTATGATGCAACACCATTTCCTTTTCAAAATGACAGGCTATA
GTCCTTGTATTCGTTCATAATGGATGTCGGCATCACCACCTCTTCTGAACTGCCAACTTGGGCTAGAACACTTAAATTAG
ATAGATCAGATTCTCATTCACCAGTAAATTGAATTTCTGAAAGTGTTAACAGGCTTTGAAACAAATAATGTTTGAAATTA
AAAAAGCAAAAACAGCCTTGAACAGATGGTTTGCATTGCTGTGGAAGATACTGATTGTTGCCCTTAAAAGTGCTAAGAAA
CATCTAGATCTTTCACCTTGACTATACTGGATAATCTGTGCCAATAAGTCATGACTCTGGAGAGACCCCTAAAATGCAAT
AGTTGTTGCTTCTCTAGCTGCCTCAAGCTGACAGAAATCCAAACTATTCCTGGTGTGCTGAAAAGTTATGTGACTTAGAA
C

Alignment

ORF - retro_rnor_1962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.87 %
• Parental protein coverage: 59.4 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QTGYTVSTTGHESYAAARLPTQNNQTIVL-INTQWMPAPPPLLNCPPGLEYLNQIDQILIHQQVELLEVL
          Q.GYT..T.G...Y.A...P.QN.....L.I...WM.A.PPLLNC..GLE.LN.IDQILIHQ..E.L.VL
Retrocopy QAGYTLTTAGCGTYDATPFPFQNDRL*SL>IRS*WMSASPPLLNCQLGLEHLN*IDQILIHQ*IEFLKVL

Parental  TGFETNN--KFEIKNSLGQMVYVAVEDTDCCTRNCCEASRPFTLRILDHLGQEVMTLERPLRCSSCCFPC
          TGFETNN......KNSL.QMV..AVEDTDCC...C.E.SR.FTL.ILD.L.Q.VMTLERPL.C.SCCF..
Retrocopy TGFETNNV*N*KSKNSLEQMVCIAVEDTDCCP*KC*ETSRSFTLTILDNLCQ*VMTLERPLKCNSCCFSS

Parental  CLQEIEIQAPPGVPIGYVTQN
          CL...EIQ..PGV...YVT.N
Retrocopy CLKLTEIQTIPGVLKSYVT*N

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	1.65 RPM
SRP017611_kidney	0.00 RPM	118.28 RPM
SRP017611_liver	0.00 RPM	1.28 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1962 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1962 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1962 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000027005	1 retrocopy	retro_fcat_797,
Myotis lucifugus	ENSMLUG00000008749	1 retrocopy	retro_mluc_1779,
Monodelphis domestica	ENSMODG00000021248	2 retrocopies	retro_mdom_1443, retro_mdom_1597,
Rattus norvegicus	ENSRNOG00000033412	1 retrocopy	retro_rnor_1962 ,