RetrogeneDB ID: retro_ocun_243

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:106545910..106546534(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000006972
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: UBE2E1
• Ensembl ID: ENSOCUG00000006026
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2E 1 [Source:HGNC Symbol;Acc:12477]

Sequence

>retro_ocun_243
ATGTGCAGTGATAGGCAGAGGTCCGACGATGAGAGCCCCAGCACCAGCAGTGGCAGTTCAGATGCGGACCAGAGAGACCC
AGCCGCTCCAGAGCCTGAGGAACAAGAAGAAAGAAAACCTTCTGCTACCCAGCAGAAGAAGAACACCAAACTCTCTAGCA
AAACCACTGCTAAGTTATCCACTAGTGCTAAAAGAATTCAGAAGGAGCTAGCTGAAATAACCCTTGATCCTCCTCCTAAT
TGTAGTGCTGGGCCTAAAGGAGATAACATTTATGAGTGGAGTTCAACTATACTTGGTCCACCAGGTTCTGTATATGAAGG
TGGTGTGTTTTGTCTGGATATCCCATTTTCATCAGATTATCCATTTAAACCACCAAAGGTTACTTTCCGCACCAGAATCT
ATCACTGCAACATCAACAGTCAGGGAGTCATCTGTTTGGACATCCTTAAAGACAACTGGAGTCCTGCTTTGACTATTTCA
AAGGTTTTGCTGTCTATTTGTTCACTTTTGACAGACTGCAACCCTACAGATCCTCTGGTTGGAAGCATAGTCACTCAGTA
TTTGACCAACAGAGCAGAACATGACAGGATAGCCAGACAGTGGACCAAGAGATACGCAACATAA

Alignment

ORF - retro_ocun_243 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.65 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SDDDSRASTSSSSSSSSNQQTEKETNTPKKKESKVSMSKNSKLLSTSAKRIQKELADITLDPPPNCSAGP
          SD.D.R............Q...K...T..KK..K.S.SK....LSTSAKRIQKELA.ITLDPPPNCSAGP
Retrocopy SDADQR---DPAAPEPEEQEERKPSATQQKKNTKLS-SKTTAKLSTSAKRIQKELAEITLDPPPNCSAGP

Parental  KGDNIYEWRSTILGPPGSVYEGGVFFLDITFTPEYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSP
          KGDNIYEW.STILGPPGSVYEGGVF.LDI.F...YPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSP
Retrocopy KGDNIYEWSSTILGPPGSVYEGGVFCLDIPFSSDYPFKPPKVTFRTRIYHCNINSQGVICLDILKDNWSP

Parental  ALTISKVLLSICSLLTDCNPADPLVGSIATQYMTNRAEHDRMARQWTKRYAT
          ALTISKVLLSICSLLTDCNP.DPLVGSI.TQY.TNRAEHDR.ARQWTKRYAT
Retrocopy ALTISKVLLSICSLLTDCNPTDPLVGSIVTQYLTNRAEHDRIARQWTKRYAT

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	13.63 RPM	33.61 RPM
SRP017611_kidney	9.43 RPM	17.03 RPM
SRP017611_liver	2.54 RPM	2.31 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_243 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_243 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_243 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003515	2 retrocopies	retro_amel_1117, retro_amel_483,
Ciona intestinalis	ENSCING00000006860	1 retrocopy	retro_cint_33,
Cavia porcellus	ENSCPOG00000002251	2 retrocopies	retro_cpor_1036, retro_cpor_52,
Felis catus	ENSFCAG00000024719	1 retrocopy	retro_fcat_623,
Macropus eugenii	ENSMEUG00000014517	1 retrocopy	retro_meug_2089,
Mus musculus	ENSMUSG00000021774	3 retrocopies	retro_mmus_2493, retro_mmus_2600, retro_mmus_537,
Oryctolagus cuniculus	ENSOCUG00000002610	3 retrocopies	retro_ocun_826, retro_ocun_932, retro_ocun_937,
Oryctolagus cuniculus	ENSOCUG00000006026	2 retrocopies	retro_ocun_134, retro_ocun_243 ,
Oryctolagus cuniculus	ENSOCUG00000008900	1 retrocopy	retro_ocun_1058,
Oryctolagus cuniculus	ENSOCUG00000029448	10 retrocopies	retro_ocun_1220, retro_ocun_1426, retro_ocun_1536, retro_ocun_1660, retro_ocun_1856, retro_ocun_1941, retro_ocun_261, retro_ocun_467, retro_ocun_887, retro_ocun_988,
Rattus norvegicus	ENSRNOG00000008794	3 retrocopies	retro_rnor_1632, retro_rnor_2291, retro_rnor_2343,
Sarcophilus harrisii	ENSSHAG00000001416	1 retrocopy	retro_shar_712,