RetrogeneDB ID: retro_rnor_2440

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:26219970..26221121(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Sgol1
• Ensembl ID: ENSRNOG00000022499
• Aliases: None
• Description: Protein Sgol1 [Source:UniProtKB/TrEMBL;Acc:D4A624]

Sequence

>retro_rnor_2440
GAAAATACGACCAGGGACTTTGACAATGTTCCCAGGGACTTGTCTGTGAAGACCTTACAGCAAACTGCTCTTGAAGAAAC
TGACTGTCCCTACCAAACCACAGGAGCAAGTCCTACTGTTACACCAGAAATACTGGGTTGTGATTTTGATTCAGGTAAAG
TCAACTCTACTGATGAAGTCTTACCTAGAACTGTATCTTCCCGTCAGCACTTAAGAAAAGACTTTAGTAAAGCCAGTTCA
AGAGAGGAGCCGTCCTTGGAGGTTAAAAGCAGTAGATGTAAAGACCTAACTGTAACCCTGCATAGACTTGACAATGTAGA
AAAAAATGTTTACCTGTGGAACAAGGAGCAAATTAACTTATGCCCTAGACTGATTAGCCCAGCAAAGATTACTAAAACAC
AAGAAGCCATTTCATCATCTAAGCCTGAACAAATAGAGATCAAGCATAAACGAGCGCAAAAAAGAAGAGCAGAGTAAAGA
AGAACCAACCAGAGATGCAAGTCAAACTTCTCATTGAGGAGTAAGGGCAGCAAAGGCAAAGAAAAGCAGGCTTTACTCCC
GAATTCACTGGATGAGTGTGTTGGTTCCAGTGATGCTTACGATTTCAATCTAAAAGAACGTGTTCACTACACCCCTTTCC
GACAAAAAATTATGGATGGCTCCAATAGAGAAACCGACAGCATCAACTCAGAAGTGAGTGCATGCAGTACCTCTGAGGGC
GAGTCTGACTACGACCCCTAGCTGCCTCCTTACAAGCGCTTGCAAGACTACACGGGGTCAGAGGAACCAGTTACCAGGTC
TTGCTCTAAAAGAGGCTCTAAGTATCCGGATGAGAAACGGTGGAGGAGGTGCTGCCACCCACAGTTCCCACTGGTGCCNC
CCGACCTGAGACTCAAGAGTCACCTCACCGAGGTCTAACGGGTGTCACCAATAGTTTGCGGCATCCTATAGTGAAAAGCA
GGAAGCTTTCTCTGGCTCCAAAACGGCATGAAGACAGCCCAGCAGTGTCTCTGCGCAGGTGTACCACCATCACAAGCTAT
AAAGAGCCGACACTCAATTCGAAGCTAAGAAGAGGGGACCCTTTTACAGACTTGTGTTTCTTGAATTCTATTTTCAAGCA
GAAAAAGGAAATGAGGCATCGTAAAAGAACA

Alignment

ORF - retro_rnor_2440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 74.33 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DNSTRDLSVKTLQQTALEETDCPFQTTDLCFNCSEASPTVTPETLGCDFDSDKVNSTDEVLPRTVSSRQH
          .N.TRD....................TD.......ASPTVTPE.LGCDFDS.KVNSTDEVLPRTVSSRQH
Retrocopy ENTTRDFDNVPRDLSVKTLQQTALEETDCPYQTTGASPTVTPEILGCDFDSGKVNSTDEVLPRTVSSRQH

Parental  LRRDFSNVSKASSREEPSLEVKRSRCKDLTVTLHRLDNIEQNVYLWNKEQINLCPRLISPAKITKTQEAI
          LR.DF...SKASSREEPSLEVK.SRCKDLTVTLHRLDN.E.NVYLWNKEQINLCPRLISPAKITKTQEAI
Retrocopy LRKDF---SKASSREEPSLEVKSSRCKDLTVTLHRLDNVEKNVYLWNKEQINLCPRLISPAKITKTQEAI

Parental  SSSKPEQKEIKHKRAQKRRAEHRRTNQRCKSNFSLRSKGSRGKEKRALPRNSLDGCVGSSDAYDFNLKER
          SSSKPEQ.EIKHKRAQKRRAE.RRTNQRCKSNFSLRSKGS.GKEK.AL..NSLD.CVGSSDAYDFNLKER
Retrocopy SSSKPEQIEIKHKRAQKRRAE*RRTNQRCKSNFSLRSKGSKGKEKQALLPNSLDECVGSSDAYDFNLKER

Parental  VHHTPFRQKMKDGSNRETDSINSEVSACSTSEGESDDDDPYLPPYKRLQDYTGSEEPVTRPRSKRGSTYP
          VH.TPFRQK..DGSNRETDSINSEVSACSTSEGES.D.DP.LPPYKRLQDYTGSEEPVTR..SKRGS.YP
Retrocopy VHYTPFRQKIMDGSNRETDSINSEVSACSTSEGES-DYDP*LPPYKRLQDYTGSEEPVTRSCSKRGSKYP

Parental  DEK-AVEEVLPPTAPTGTP-PETQESPHRGLKDVTNSLRRPIVKSRKLSLAPKRHEDSPAVSLRRCTTII
          DEK..VEEVLPPT.PTG...PETQESPHRGL..VTNSLR.PIVKSRKLSLAPKRHEDSPAVSLRRCTTI.
Retrocopy DEK<TVEEVLPPTVPTGAXRPETQESPHRGLTGVTNSLRHPIVKSRKLSLAPKRHEDSPAVSLRRCTTIT

Parental  SYKEPTLNSKLRRGDPFTDLCFLNSPIFKQKKEMRHRKRT
          SYKEPTLNSKLRRGDPFTDLCFLNS.IFKQKKEMRHRKRT
Retrocopy SYKEPTLNSKLRRGDPFTDLCFLNS-IFKQKKEMRHRKRT

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	0.58 RPM
SRP017611_kidney	0.00 RPM	0.14 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2440 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2440 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2440 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013948	1 retrocopy	retro_chof_2699,
Dasypus novemcinctus	ENSDNOG00000008694	1 retrocopy	retro_dnov_1045,
Equus caballus	ENSECAG00000012475	1 retrocopy	retro_ecab_846,
Mus musculus	ENSMUSG00000023940	2 retrocopies	retro_mmus_3486, retro_mmus_867,
Rattus norvegicus	ENSRNOG00000022499	1 retrocopy	retro_rnor_2440 ,