RetrogeneDB ID: retro_rnor_2668

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:23797916..23798634(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Prmt1
• Ensembl ID: ENSRNOG00000026109
• Aliases: Prmt1, Hrmt1l2
• Description: Protein arginine N-methyltransferase 1 [Source:UniProtKB/Swiss-Prot;Acc:Q63009]

Sequence

>retro_rnor_2668
ATGGTGGAAGCTGAGTCAGTGAATTGCATCATGGAGGTTTCCTATGGCCAAGCAGAAAATAGTGTGAAGCCCAGCACTGA
GGACATGACATCCAAAGACTACTTACTTTGACTCCTATCCCCACCTTGACATCCATGAGGAAATGCTAACAGATGAGTTG
CTTATCCTCACACACCACAACTCCATGTTTCACAATCGGCAATTTTTCAAAGATGAGGTGCTGGATGTGGGGCTCAGGCA
CTGGCATCCTCTGCATGTTTGCTGCCAAGAAAAGGACCTGCTAGGTTTTGGGTATAGAGTGTTCCAGTATCTCTGATTAT
GCTGTGAAGATGGTCAAACCAATAAGTTAGACTATAGGCTGTTCACCATCAAAGGCAAGGTGGAGGAGGTGGAGCGTCCG
TGGAGAAGGTGGACATCATCAGCAGCAAGTGGATGGGTTATTGCCTCAATGAGTACACGCTCAACATCATGCTGCATGCT
CATGACAAGTAGCTGGTACATGATGGCCTCATTTTCCCAGACCGGGTCACCCTGTATGTGACAATCATTGAGGACCAACA
GTATAAAGACTACAAGATGCACTGGTGGGAGAATATGTATGGTTTTGATAAAGTCCTGCATTAAAGACATAGCTATCAAG
GTCTCCCTGGTATACATGGTGGAACCAAAATAGGTGGTCACCAATGTCTGCCTCATAATGGAAGTGGACATCTACAGT

Alignment

ORF - retro_rnor_2668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.54 %
• Parental protein coverage: 68.27 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MAAAEAANCIMEVSCGQAESSEKPNAEDMTSKDY-YFDSYAHFGIHEEMLKDEVRTLTYRNSMFHNRHLF
          M..AE..NCIMEVS.GQAE.S.KP..EDMTSKDY.YFDSY.H..IHEEML.DE...LT..NSMFHNR..F
Retrocopy MVEAESVNCIMEVSYGQAENSVKPSTEDMTSKDY>YFDSYPHLDIHEEMLTDELLILTHHNSMFHNRQFF

Parental  KDKVVLDVG-SGTGILCMFAAKAGARKVIGIECSSISDYAVKIVK-ANKLDHVVTIIKGKVEEVELP-VE
          KD.V.LDVG.SGTGILCMFAAK.....V.GIECSSISDYAVK.VK..NKLD.....IKGKVEEVE.P.VE
Retrocopy KDEV-LDVG>SGTGILCMFAAKKRTC*VLGIECSSISDYAVKMVK<TNKLDYRLFTIKGKVEEVERP<VE

Parental  KVDIIISEWMGYCLFYESMLNTVLHARDKWLAPDGLIFPDRATLYVTAIEDRQYKDYKIHWWENVYGFD-
          KVDII.S.WMGYCL..E..LN..LHA.DK.L..DGLIFPDR.TLYVT.IED.QYKDYK.HWWEN.YGFD.
Retrocopy KVDIISSKWMGYCL-NEYTLNIMLHAHDK*LVHDGLIFPDRVTLYVTIIEDQQYKDYKMHWWENMYGFD>

Parental  MSCIKDVAIKEPLVDVVDPKQLVTNACLIKEVDIYT
          .SCIKD.AIK..LV..V.PK..VTN.CLI.EVDIY.
Retrocopy KSCIKDIAIKVSLVYMVEPK*VVTNVCLIMEVDIYS

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	20.56 RPM
SRP017611_kidney	0.00 RPM	14.72 RPM
SRP017611_liver	0.00 RPM	4.10 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2668 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2668 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2668 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003670	3 retrocopies	retro_cjac_1800, retro_cjac_1979, retro_cjac_764,
Danio rerio	ENSDARG00000010246	1 retrocopy	retro_drer_7,
Felis catus	ENSFCAG00000006081	1 retrocopy	retro_fcat_1762,
Homo sapiens	ENSG00000126457	1 retrocopy	retro_hsap_3406,
Gasterosteus aculeatus	ENSGACG00000004897	1 retrocopy	retro_gacu_2,
Gorilla gorilla	ENSGGOG00000000503	1 retrocopy	retro_ggor_2305,
Macaca mulatta	ENSMMUG00000003029	1 retrocopy	retro_mmul_2121,
Otolemur garnettii	ENSOGAG00000011938	2 retrocopies	retro_ogar_2471, retro_ogar_2929,
Rattus norvegicus	ENSRNOG00000026109	2 retrocopies	retro_rnor_1077, retro_rnor_2668 ,