RetrogeneDB ID: retro_rnor_621

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:179376170..179377315(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Skp2
• Ensembl ID: ENSRNOG00000016823
• Aliases: Skp2, RGD1562456
• Description: S-phase kinase-associated protein 2 [Source:RefSeq peptide;Acc:NP_001099886]

Sequence

>retro_rnor_621
ATGCATAAGAAGCACCTTCAGGAGATTCCAGACCAGAGTAGCAACGTCACCACCAGCTTCACGTGGGGATGGGATTCCAG
CAAGACTTCTGAACTGCTGTCAGGCATGGGTGTCTCTGCCTTGGAGAAGGAAGAGGTGGACAGTGAGAACATCCCACATG
GACTGCTCTCAAACCTCTGCCACCCCCAGAGCCCTCCAAGGAAAAGGCTAAAGAGCAAAGCGAGTGACAAAGACTTTGTG
ATCATCCGTCGGCCTAAGCTCAATAGAGAGAACTTTCCAGGTGTTTCCTGGGACTCCCTTCCAGATGAACTGCTCCTGGG
GATCTTTTCCTGTCTGTGTCTCCCTGAGCTTTTGAGAGTCTCTGGAGTTTGCAAGAGGTGGTACCGCCTCTCGCTCGACC
AGTCTCTCTGGCAGTCTCTAGACCTCGCAGGCAAAATCTGCACCCAGAACTGACTGTGCGCTTGCTCTCTCGAGAAGTTG
TGGCCTTCCGCTGCCCACGGTCGTTTATGGAGCAGCCACTGGGTGAAAGCTTCAGCTCTTTCCGTGTACAGCACATGGAA
CTGTCGAACTCAGTTATAAATATGTCAAACCTCCAGGGGATTCTGTCTCAGTGCTCCAAGCTGCAGAATCTGAGTCTGGA
AAGCCTGCAGCTTTCAGATCCCATTGTCACTACTCTTGCATAGAATGAAAACTTGGTGCGACTGAACCTTTGTGGGTGCT
CTGGATTTTCAGAGTTTGCGGTGGCCACCCTGCTGAACAGCTGCTCCAGACTGAATGAACTGAATCTCTCCTGGTGCTTT
GACTTTACTGAAAAGCATGTGCAAGCGGCTGTGGCACATTTACCAGACACCCTCATCCAGCTGAACCTCAGTGGTTACCG
AAAGAACCTCCAGAAAACAGATCTTTGTACCGTAATTAAACGATACCCCAACCTCGTCCGCCTCAACTTAAGTGACAATA
TCATGCTAAAGAACGACTGCTTTCCCGAATTTTTTCAACTCAACTACCTCCAACACCTCTCGCTCAGCCAGTGCAATGAT
ATAATACCTGAGACTCTACTTGAACTCGGAGAAATCCCCACACTAAAAACACTACAAGTTTTTGGAATCGTGCCAGATGG
GACCCTTCAGCTACTGAGAAGCTCT

Alignment

ORF - retro_rnor_621 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.21 %
• Parental protein coverage: 90.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MHRKHLQEIPDQSSNVTTSFTWGWDSSKTSELLSGMGVSALEKEEVDSENIPHGLLSNLGHPQSPPRKRL
          MH.KHLQEIPDQSSNVTTSFTWGWDSSKTSELLSGMGVSALEKEEVDSENIPHGLLSNL.HPQSPPRKRL
Retrocopy MHKKHLQEIPDQSSNVTTSFTWGWDSSKTSELLSGMGVSALEKEEVDSENIPHGLLSNLCHPQSPPRKRL

Parental  KSKGSDKDFVIIRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLRVSGVCKRWYRLSLDESLWQSL
          KSK.SDKDFVIIRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLRVSGVCKRWYRLSLD.SLWQSL
Retrocopy KSKASDKDFVIIRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLRVSGVCKRWYRLSLDQSLWQSL

Parental  DLAGK-NLHPDVTVRLLSRGVVAFRCPRSFMEQPLGESFSSFRVQHMDLSNSVINVSNLHGILSECSKLQ
          DLAGK.NLHP..TVRLLSR.VVAFRCPRSFMEQPLGESFSSFRVQHM.LSNSVIN.SNL.GILS.CSKLQ
Retrocopy DLAGK<NLHPELTVRLLSREVVAFRCPRSFMEQPLGESFSSFRVQHMELSNSVINMSNLQGILSQCSKLQ

Parental  NLSLEGLQLSDPIVTTLAQNENLVRLNLCGCSGFSESAVATLLSSCSRLDELNLSWCFDFTEKHVQAAVA
          NLSLE.LQLSDPIVTTLA.NENLVRLNLCGCSGFSE.AVATLL.SCSRL.ELNLSWCFDFTEKHVQAAVA
Retrocopy NLSLESLQLSDPIVTTLA*NENLVRLNLCGCSGFSEFAVATLLNSCSRLNELNLSWCFDFTEKHVQAAVA

Parental  HLPDTLTQLNLSGYRKNLQKTDLCTLIKRCPNLVRLDLSDSIMLKNDCFPEFFQLNYLQHLSLSRCYDII
          HLPDTL.QLNLSGYRKNLQKTDLCT.IKR.PNLVRL.LSD.IMLKNDCFPEFFQLNYLQHLSLS.C.DII
Retrocopy HLPDTLIQLNLSGYRKNLQKTDLCTVIKRYPNLVRLNLSDNIMLKNDCFPEFFQLNYLQHLSLSQCNDII

Parental  PETLLELGEIPTLKTLQVFGIVPDGTLQLLREA
          PETLLELGEIPTLKTLQVFGIVPDGTLQLLR..
Retrocopy PETLLELGEIPTLKTLQVFGIVPDGTLQLLRSS

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	5.61 RPM
SRP017611_kidney	0.00 RPM	3.21 RPM
SRP017611_liver	0.00 RPM	1.88 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_621 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_621 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_621 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013562	4 retrocopies	retro_btau_1108, retro_btau_1612, retro_btau_525, retro_btau_555,
Callithrix jacchus	ENSCJAG00000018275	1 retrocopy	retro_cjac_2367,
Cavia porcellus	ENSCPOG00000013303	1 retrocopy	retro_cpor_1166,
Nomascus leucogenys	ENSNLEG00000016025	1 retrocopy	retro_nleu_2553,
Oryctolagus cuniculus	ENSOCUG00000009154	1 retrocopy	retro_ocun_158,
Pelodiscus sinensis	ENSPSIG00000008375	1 retrocopy	retro_psin_28,
Rattus norvegicus	ENSRNOG00000016823	1 retrocopy	retro_rnor_621 ,