RetrogeneDB ID: retro_rnor_2496

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:6462123..6462629(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2g1
• Ensembl ID: ENSRNOG00000010041
• Aliases: Ube2g1, Ubc7
• Description: Ubiquitin-conjugating enzyme E2 G1 [Source:UniProtKB/Swiss-Prot;Acc:P62255]

Sequence

>retro_rnor_2496
ATGACAGAGCTGTAGTCATTGTTGCTACTGCGAAGACAGCAGGCAGAACTCAACAAAAATACAGTGGAAGGCATTTCAGC
AGGTTTAATAGATGACAATGTTCTCTATCGTTGGCAAGTCCTTATTATTTGTCCTCCAGATACACTTTGTGTAGGTGGTA
TTTTTAAGGCTCATCTCATTTCCCAAAAGATTATCCCCTCCAGTTTCTTACATGAAATTCATTACAGAGATTTGGCACCC
AAATGTTGATAAAATTGGTAATGTTTGCATTTCTATTCTTCATGAGTTTGAGGAGGATAAGTATGGTTATGAGAAGGCAG
AGGAATGATGGCTGCCTGTCCATACTGTGGAAACCATCATGATTATTGTCAGTTCTATGCTGCAGATCCTAATGGAGACT
CACCTGCAAATGTAGATGCTGTGACGGAATGGAGGGAAGACAGAAATGCAGAATTTCAAAGGCGAGTTGCCACTGTGTAA
GGAAAAGCCAAGAAACTGCTTTTGAG

Alignment

ORF - retro_rnor_2496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MTELQSALLLRRQLAELNKNPVEGFSAGLIDDNDLYRWEVLIIGPPDTLYEGGVFKAHLT-FPKDYPLR-
          MTEL.S.LLLRRQ.AELNKN.VEG.SAGLIDDN.LYRW.VLII.PPDTL..GG.FKAHL..FPKDYPL..
Retrocopy MTEL*SLLLLRRQQAELNKNTVEGISAGLIDDNVLYRWQVLIICPPDTLCVGGIFKAHLI<FPKDYPLQ<

Parental  PPKMKFITEIWHPNVDKNGDVCISILHEPGEDKYGYEKPEERWLPIHTVETIMISVISML-ADPNGDSPA
          ...MKFITEIWHPNVDK.G.VCISILHE..EDKYGYEK.EE.WLP.HTVETIMI.V.SML.ADPNGDSPA
Retrocopy VSYMKFITEIWHPNVDKIGNVCISILHEFEEDKYGYEKAEE*WLPVHTVETIMIIVSSML<ADPNGDSPA

Parental  NVDAAKEWREDRNGEFKRKVA-RCVRKSQETAFE
          NVDA..EWREDRN.EF.R.VA..CVRKSQETAFE
Retrocopy NVDAVTEWREDRNAEFQRRVA<HCVRKSQETAFE

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	41.70 RPM
SRP017611_kidney	0.00 RPM	48.08 RPM
SRP017611_liver	0.00 RPM	30.86 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2496 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2496 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2496 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014433	1 retrocopy	retro_btau_604,
Choloepus hoffmanni	ENSCHOG00000011801	1 retrocopy	retro_chof_2181,
Ciona savignyi	ENSCSAVG00000009498	1 retrocopy	retro_csav_4,
Macropus eugenii	ENSMEUG00000009769	3 retrocopies	retro_meug_360, retro_meug_473, retro_meug_647,
Myotis lucifugus	ENSMLUG00000002118	1 retrocopy	retro_mluc_104,
Oryctolagus cuniculus	ENSOCUG00000000248	1 retrocopy	retro_ocun_152,
Otolemur garnettii	ENSOGAG00000008795	1 retrocopy	retro_ogar_2554,
Rattus norvegicus	ENSRNOG00000008348	1 retrocopy	retro_rnor_1464,
Rattus norvegicus	ENSRNOG00000010041	3 retrocopies	retro_rnor_2496 , retro_rnor_317, retro_rnor_970,
Rattus norvegicus	ENSRNOG00000010727	1 retrocopy	retro_rnor_1508,
Sarcophilus harrisii	ENSSHAG00000002399	1 retrocopy	retro_shar_75,
Tupaia belangeri	ENSTBEG00000006117	1 retrocopy	retro_tbel_2852,
Tetraodon nigroviridis	ENSTNIG00000008566	1 retrocopy	retro_tnig_11,
Takifugu rubripes	ENSTRUG00000005995	1 retrocopy	retro_trub_4,
Tursiops truncatus	ENSTTRG00000000595	1 retrocopy	retro_ttru_1578,
Drosophila melanogaster	FBgn0058045	1 retrocopy	retro_dmel_6,