RetrogeneDB ID: retro_rnor_297

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:11568935..11570054(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000023261
• Aliases: Ube2q2l, RGD1563226
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ube2q1
• Ensembl ID: ENSRNOG00000020791
• Aliases: Ube2q1, Ube2q
• Description: ubiquitin-conjugating enzyme E2 Q1 [Source:RefSeq peptide;Acc:NP_001099918]

Sequence

>retro_rnor_297
ATGTCGTCGGGGCTTAAGGCCGAGCTGGAGTTCCTAGCGTCCATCTTCGACAAGGACCACGAGCGGCTGCGCATCGTGAG
CTGGCAGCTGGATGAGCTGCAGTGTCAGTTCCTGGTGCCGCCGGCGCCCGCGGGCAGCCCGCCCTTGCCGCCGCCGCTCA
CCCTGCACTGCACCATCACCGAGTCCTACCCATCCTCGCCGCCGATATGGTTCGTGGACTCTGACGATCCAGACCTCACA
TCGATCCTGGAACGTCTGGAAGATTCGAAGCCCAACAGTTCGCTTCGTCAGCAGCTCAAGTGGCTGATCTGCGAACTCTG
CAGCTTATATAACCTGCCTGAGCACCTGGATGTGAAGATGCTGGACCAGCCGGTCCCCATCGCCCAGAAAGCGACCATCG
AGGAGGTGCCTTCTGAAGATGAAGAGGAAGATGCAGCTGACGGGCTGGAAGACTTGGATCATTATGAGCTGAAAGAAGAT
ACTTGTAGTGAGAAAAAGTCAGAGGATGAAGGGCTTGAGAAAGAGCATTTGGCAATATTAGAGAATATCAAGAAGAGCCA
AAGGCAAGAGCATTTGAATGGTACCGTGTCTGGCTCAGTGCATGCTTCAAATAGACTCATGAAAGAACTCAGAGAGATAT
ACAGGTCGCAGAGTTACAAGTCGGGGACTTATTCTGTGGAACTGATAAACGACAGCTTATATGACTGGCACGTTAAACTG
AGGAAGGTTGACCCCGATAGTCCCTTGTACGGCGACCTTCAGCTCTTGAAAGAAAAAGAAGGCATAGAATATATTTTGCT
TAACTTTTCTTTCAAAGATAACTTTCCGTTTGATCCTCCCTTTGTTCGCGTCGAGTTGCCCATTCTCTCTGGAGGGTATG
TCTTGGGCGGAGGGGCATTGTGTATGGAACTGCTCACCAAGCAGGGCTGGAGCAGCGCGTACTCCATAGAATCGGTTATT
ATGCAGATCAACGCCACCCTAGTCAAAGGCAAGGCCAGGGTGCGCTTTGGAGCAGATAAGAATCAATATAATCTAGAAAC
AGCCCAACAGTCCTATGACTCTGTCGTGCAGATGCATGAGAAAAAAGGCTGGTTCACTCCTCCAAAGGAAGATGGGTAA

Alignment

ORF - retro_rnor_297 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.55 %
• Parental protein coverage: 79.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PHLPSRGSVPGDPVRIHCNITESYPAVPPIWSVESDDPNLAAVLERLVDIKKGNTLLLQHLKRIISDLCK
          P..P........P...HC.ITESYP..PPIW.V.SDDP.L...LERL.D..K.N..L.Q.LK..I..LC.
Retrocopy PPAPAGSPPLPPPLTLHCTITESYPSSPPIWFVDSDDPDLTSILERLED-SKPNSSLRQQLKWLICELCS

Parental  LYNLPQHPDVEMLDQPLP-AEQCTQEEVSSEDEDEEMPEDTEDLDHYEMKEEEPAEGKKSEDDGIGKENL
          LYNLP.H.DV.MLDQP.P.A...T.EEV.SEDE.E......EDLDHYE.KE....E.KKSED.G..KE.L
Retrocopy LYNLPEHLDVKMLDQPVPIAQKATIEEVPSEDEEEDAADGLEDLDHYELKEDTCSE-KKSEDEGLEKEHL

Parental  AILEKIKKNQRQDYLNGAVSGSVQATDRLMKELRDIYRSQSFKGGNYAVELVNDSLYDWNVKLLKVDQDS
          AILE.IKK.QRQ..LNG.VSGSV.A..RLMKELR.IYRSQS.K.G.Y.VEL.NDSLYDW.VKL.KVD.DS
Retrocopy AILENIKKSQRQEHLNGTVSGSVHASNRLMKELREIYRSQSYKSGTYSVELINDSLYDWHVKLRKVDPDS

Parental  ALHNDLQILKEKEGADFILLNFSFKDNFPFDPPFVRVVSPVLSGGYVLGGGAICMELLTKQGWSSAYSIE
          .L..DLQ.LKEKEG...ILLNFSFKDNFPFDPPFVRV..P.LSGGYVLGGGA.CMELLTKQGWSSAYSIE
Retrocopy PLYGDLQLLKEKEGIEYILLNFSFKDNFPFDPPFVRVELPILSGGYVLGGGALCMELLTKQGWSSAYSIE

Parental  SVIMQISATLVKGKARVQFGANKSQYSLTRAQQSYKSLVQIHEKNGWYTPPKEDG
          SVIMQI.ATLVKGKARV.FGA.K.QY.L..AQQSY.S.VQ.HEK.GW.TPPKEDG
Retrocopy SVIMQINATLVKGKARVRFGADKNQYNLETAQQSYDSVVQMHEKKGWFTPPKEDG

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	6.47 RPM	83.33 RPM
SRP017611_kidney	0.49 RPM	62.39 RPM
SRP017611_liver	0.34 RPM	30.26 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_297 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_297 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_297 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_3421

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008889	1 retrocopy	retro_dnov_449,
Macropus eugenii	ENSMEUG00000003718	2 retrocopies	retro_meug_1816, retro_meug_358,
Microcebus murinus	ENSMICG00000001427	1 retrocopy	retro_mmur_339,
Rattus norvegicus	ENSRNOG00000020791	1 retrocopy	retro_rnor_297 ,
Tupaia belangeri	ENSTBEG00000013007	1 retrocopy	retro_tbel_3091,
Tursiops truncatus	ENSTTRG00000013998	1 retrocopy	retro_ttru_975,