RetrogeneDB ID: retro_rnor_2682

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:50089731..50090585(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Golph3l
• Ensembl ID: ENSRNOG00000047620
• Aliases: None
• Description: Golgi phosphoprotein 3-like [Source:UniProtKB/Swiss-Prot;Acc:Q66H74]

Sequence

>retro_rnor_2682
ATGTCAACATTAACTCACCGGACCAGTTGAACTGAAGTAAGTAAGAGCTCTGAAGAGAAAATAGAAAGCGAGGAAGACAC
TAATCAAGAAAAGAGTCCAGATAATGAAGACCCTGGAGACTCTACGGATATCTGCCTCACTCTTACGGAAGAAGTATTGC
TCCTGGGACTAAGAGATAAAGAGGGCTACGCATCTTTCTGGAATGAGTGTTTATCACCTGGGCTTCGAGGAGGCATCCCG
ATAGAGCTGGCCATACTGGGTAGACTCTATCTGGATCCTCCCACCATGCATAAGAAGAGACTCCCAGACAGAAAGGTCCT
GCTAAAGTCAGCCAGCCCAACAGGTGATGTTTTGCTGGATGAAATGCTCACACACATTAAAGCAACTGAGCCAGCAGAAA
CTGTGCAGACATGGATCGAGCTACTCACTGGTGAGACATGGAACCCCTTCAAATTACAGTACCAGCTGAGAAATGTACGA
GAACGAATTGCCAAGAACCTGGCAGAAAAGGGTATTCTAACCACAGAGAAGCAGAATCTCCTGCTGTTCGACATGACCAC
TTATCCAGTGATTAATACAAGAGAGAAATAGTGACAAATGAAAAGCTTCAAGACAGTGTGCTGGAACGGTGGGTAAACGA
CCCTCAGGGCATGGACGGGCGAACACTGGCGCTCCTGGTGCTGGCCCACTCCTCCGATGTCCTGGAGAACGTCTTCTCTT
GTCTTACAGATGATAAGTATGATGTGGCAATGAATTGAACCAACGACCTAGTAGAACTGGACCCTGAAGTGGAAGGGACA
AAGCACAATACCACAGAGACGATCTGGGCTGTGCTGGCAGCTTTCAACAAATCC

Alignment

ORF - retro_rnor_2682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.01 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTTLTHRTRRTEVSKSCEKKIESEEDTNQERSPDNEDPGDSKDIRLTLMEEVLLLGLKDKEGYTSFWNDC
          M.TLTHRT..TEVSKS.E.KIESEEDTNQE.SPDNEDPGDS.DI.LTL.EEVLLLGL.DKEGY.SFWN.C
Retrocopy MSTLTHRTS*TEVSKSSEEKIESEEDTNQEKSPDNEDPGDSTDICLTLTEEVLLLGLRDKEGYASFWNEC

Parental  ISSGLRGGILIELAMRGRIYLEPPTMRKKRLLDRKVLLKSDSPTGDVLLDETLKHIKATEPTETVQTWIE
          .S.GLRGGI.IELA..GR.YL.PPTM.KKRL.DRKVLLKS.SPTGDVLLDE.L.HIKATEP.ETVQTWIE
Retrocopy LSPGLRGGIPIELAILGRLYLDPPTMHKKRLPDRKVLLKSASPTGDVLLDEMLTHIKATEPAETVQTWIE

Parental  LLTGETWNPFKLQYQLRNVRERIAKNLVEKGILTTEKQNFLLFDMTTHPVTNTTEKQRLMK-KLQDSVLE
          LLTGETWNPFKLQYQLRNVRERIAKNL.EKGILTTEKQN.LLFDMTT.PV.NT.EK...MK.KLQDSVLE
Retrocopy LLTGETWNPFKLQYQLRNVRERIAKNLAEKGILTTEKQNLLLFDMTTYPVINTREK**QMK<KLQDSVLE

Parental  RWVNDPQRMDRRTLALLVLAHSSDVLENVFSCLTDDKYDVAMNRTKDLVELDPEVEGTKHNATEMIWAVL
          RWVNDPQ.MD.RTLALLVLAHSSDVLENVFSCLTDDKYDVAMN.T.DLVELDPEVEGTKHN.TE.IWAVL
Retrocopy RWVNDPQGMDGRTLALLVLAHSSDVLENVFSCLTDDKYDVAMN*TNDLVELDPEVEGTKHNTTETIWAVL

Parental  AAFNKS
          AAFNKS
Retrocopy AAFNKS

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	0.07 RPM	9.78 RPM
SRP017611_kidney	0.14 RPM	16.47 RPM
SRP017611_liver	0.00 RPM	7.67 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2682 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2682 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2682 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
Bos taurus	ENSBTAG00000020357	1 retrocopy	retro_btau_1256,
Choloepus hoffmanni	ENSCHOG00000013505	2 retrocopies	retro_chof_1173, retro_chof_1603,
Myotis lucifugus	ENSMLUG00000003484	1 retrocopy	retro_mluc_1551,
Rattus norvegicus	ENSRNOG00000047620	1 retrocopy	retro_rnor_2682 ,