RetrogeneDB ID: retro_rnor_1236

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:59055147..59055767(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ube2e3
• Ensembl ID: ENSRNOG00000004544
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2 E3 [Source:RefSeq peptide;Acc:NP_001041322]

Sequence

>retro_rnor_1236
ATGTCCAGTGATAGCCAAAGGTTGGACGATGAGAGCCCCAACACCAGCAGTGGCAGTTCAGATGCAGACCAGCGAGACCC
TATCACTCCAGAGTCTGAGAAACAGGAAGAAAGAAAACCTCTGTCACCCAGAAGAAGAAAAGCACCAAACTCTATAGCAA
AATGACTGCTAAGTTATCCACTAGTGCTGAGAGAATTCAGAGGGAGCTAGCTGAGCTCACCCTTGGTCTTCCCCCTAACT
GCAGTGCTGGGCCTAAGGAGATAACATTTAAAGAATGGAGGCCAACTCTACTTGGTCCACCAGGTTCTGTCTATGAAGGT
GGTGGGTTTTTTTTTCTTCTTCTTGATTTCACGTTCTCTTCAGATGATCCATTTAAGCCACCAAAGGTTACCTTCTATAC
CCGAATCTATCACTGTAATATCAACCGTCAGGGAGTCCTCTGCCTGGATATTCTGAAAGACAACTGGAGTCCTGCTTTGA
CTATTTCAAAGGTTTTGCTCTCTATCTGTTCCCTTTTGACAGACTGCAACCCTTTGGATCCTCTGGTTGGAAGCATAGCC
ACTCAGTATTTGAGCAACAGAGTAGAACATGACAGGATAGCCAGACAGAGATATGCAACG

Alignment

ORF - retro_rnor_1236 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSDRQRSDDESPSTSSGSSDADQRDPAAPEPEEQEERKP-SATQQKKNTKLSSKTTAKLSTSAKRIQKE
          MSSD.QR.DDESP.TSSGSSDADQRDP..PE.E.QEERKP.S.TQ.KK.TKL.SK.TAKLSTSA.RIQ.E
Retrocopy MSSDSQRLDDESPNTSSGSSDADQRDPITPESEKQEERKP<SVTQKKKSTKLYSKMTAKLSTSAERIQRE

Parental  LAEITLDPPPNCSAGPKGDNIYEWRSTILGPPGSVYEGG---VFFLDITFSSDYPFKPPKVTFRTRIYHC
          LAE.TL..PPNCSAGPK.....EWR.T.LGPPGSVYEGG......LD.TFSSD.PFKPPKVTF.TRIYHC
Retrocopy LAELTLGLPPNCSAGPKEITFKEWRPTLLGPPGSVYEGGGXXXLLLDFTFSSDDPFKPPKVTFYTRIYHC

Parental  NINSQGVICLDILKDNWSPALTISKVLLSICSLLTDCNPADPLVGSIATQYLTNRAEHDRIARQWTKRYA
          NIN.QGV.CLDILKDNWSPALTISKVLLSICSLLTDCNP.DPLVGSIATQYL.NR.EHDRIARQ...RYA
Retrocopy NINRQGVLCLDILKDNWSPALTISKVLLSICSLLTDCNPLDPLVGSIATQYLSNRVEHDRIARQ---RYA

Parental  T
          T
Retrocopy T

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	53.78 RPM
SRP017611_kidney	0.00 RPM	32.87 RPM
SRP017611_liver	0.00 RPM	17.55 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1236 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1236 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1236 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_3123

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014163	3 retrocopies	retro_cfam_2076, retro_cfam_2161, retro_cfam_27,
Choloepus hoffmanni	ENSCHOG00000007325	3 retrocopies	retro_chof_1756, retro_chof_2077, retro_chof_2358,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Callithrix jacchus	ENSCJAG00000011559	3 retrocopies	retro_cjac_3194, retro_cjac_3911, retro_cjac_3967,
Equus caballus	ENSECAG00000007233	1 retrocopy	retro_ecab_196,
Echinops telfairi	ENSETEG00000019324	2 retrocopies	retro_etel_314, retro_etel_848,
Homo sapiens	ENSG00000170035	1 retrocopy	retro_hsap_4653,
Macaca mulatta	ENSMMUG00000008069	2 retrocopies	retro_mmul_1382, retro_mmul_1834,
Monodelphis domestica	ENSMODG00000010301	2 retrocopies	retro_mdom_1679, retro_mdom_1688,
Mus musculus	ENSMUSG00000027011	4 retrocopies	retro_mmus_2814, retro_mmus_3123, retro_mmus_3416, retro_mmus_3571,
Nomascus leucogenys	ENSNLEG00000006290	1 retrocopy	retro_nleu_2068,
Otolemur garnettii	ENSOGAG00000014956	4 retrocopies	retro_ogar_1343, retro_ogar_2512, retro_ogar_2682, retro_ogar_3443,
Pongo abelii	ENSPPYG00000012987	1 retrocopy	retro_pabe_3614,
Rattus norvegicus	ENSRNOG00000001862	4 retrocopies	retro_rnor_1602, retro_rnor_2633, retro_rnor_2799, retro_rnor_526,
Rattus norvegicus	ENSRNOG00000004544	1 retrocopy	retro_rnor_1236 ,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Rattus norvegicus	ENSRNOG00000013741	9 retrocopies	retro_rnor_2777, retro_rnor_342, retro_rnor_345, retro_rnor_539, retro_rnor_650, retro_rnor_724, retro_rnor_725, retro_rnor_772, retro_rnor_784,
Tupaia belangeri	ENSTBEG00000009932	2 retrocopies	retro_tbel_1986, retro_tbel_3294,
Tarsius syrichta	ENSTSYG00000002281	5 retrocopies	retro_tsyr_1393, retro_tsyr_1809, retro_tsyr_1842, retro_tsyr_1942, retro_tsyr_457,
Tursiops truncatus	ENSTTRG00000001361	1 retrocopy	retro_ttru_1056,