RetrogeneDB ID: retro_ocun_1564

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018700:1309550..1310381(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35A3
• Ensembl ID: ENSOCUG00000015538
• Aliases: None
• Description: solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3 [Source:HGNC Symbol;Acc:11023]

Sequence

>retro_ocun_1564
AAGATAATGGCCTGTATTTTATTAGTTTACAAAGACAACAAGTGTAGTCTAAGAGCACTGAGCTGAGTACGACACGAAGA
GATTCTTAATAAACCCATGGAAACACTTAAACTTGCTATTTCAACAGGGATATATACTCTTCAGAATAATTTGCTCTATG
TGGCTCTGTCAGATCTAGATGCAGCTGCTTATCAGGTCATGTATCAGTTGAAAATTCTTACAACAGCGTTATATTCTGTG
TCTATGCTTAGTAAAAAATTAGATGTGTACCAGTGGCTTTCCCTATTAATTTTGATGACAGGAGTTGCTTTTGTTCAGTG
GCCCTCAGATTCTCAAGAACTTGAATCTAAGGAACTTTCGGTTGGCTCTCAGTTTGTAGGCCTCATGGCAATTCTCACAG
CATGTTTTTTAAGTGGCTTTGCTGGTGTTTATTTTGAGAAAATATTAAAAGAAACTAAATAATCAGTATGGATAAGAAAC
ATTCAGCTTGGTTTCTTTGGGAGTATATTTGGATTAATGGCTATATATATTTATGATGGAGAATTGGTATCCAAGAATGG
ATTCTTTCAGGGATATAACCAATTGACCTGGATAGTTGTTGCTCTTCAGGCACTTGGAGGCCATGTAGTGGCTGCTGTTA
TTAAGTATGTGGATAATATTTTAAAAGGATTCGCAACGTCTTTGTCTATAATATTATCAACACTGATATCCTATTTTTGG
CTACAAGATTTTGTGCCAATGAGTGTCTTTTTCCTTGGAGCCATCCTTGTAATAACAGCTACTTTCTTATATGGTTATGA
TCCCAAGACTGCAGGAAACCTCACTAAAGCA

Alignment

ORF - retro_ocun_1564 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.42 %
• Parental protein coverage: 78.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KIMACILLVYKDNKCSLRALNRVLHDEILNKPMETLKLAIPSGIYTLQNNLLYVALSNLDAATYQVTYQL
          KIMACILLVYKDNKCSLRAL..V.H.EILNKPMETLKLAI..GIYTLQNNLLYVALS.LDAA.YQV.YQL
Retrocopy KIMACILLVYKDNKCSLRALS*VRHEEILNKPMETLKLAISTGIYTLQNNLLYVALSDLDAAAYQVMYQL

Parental  KILTTALFSVSMLSKKLGVYQWLSLLILMTGVAFVQWPSDSQELDSKELSAGSQFVGLMAVLTACFSSGF
          KILTTAL.SVSMLSKKL.VYQWLSLLILMTGVAFVQWPSDSQEL.SKELS.GSQFVGLMA.LTACF.SGF
Retrocopy KILTTALYSVSMLSKKLDVYQWLSLLILMTGVAFVQWPSDSQELESKELSVGSQFVGLMAILTACFLSGF

Parental  AGVYFEKILKETKQSVWIRNIQLGFFGSIFGLMAVYIYDGELVSKNGFFQGYNQLTWIVVALQALGGLVV
          AGVYFEKILKETK.SVWIRNIQLGFFGSIFGLMA.YIYDGELVSKNGFFQGYNQLTWIVVALQALGG.VV
Retrocopy AGVYFEKILKETK*SVWIRNIQLGFFGSIFGLMAIYIYDGELVSKNGFFQGYNQLTWIVVALQALGGHVV

Parental  AAVIKYADNILKGFATSLSIILSTLISYFWLQDFVPTSVFFLGAILVITATFLYGYDPKPAGNLTKA
          AAVIKY.DNILKGFATSLSIILSTLISYFWLQDFVP.SVFFLGAILVITATFLYGYDPK.AGNLTKA
Retrocopy AAVIKYVDNILKGFATSLSIILSTLISYFWLQDFVPMSVFFLGAILVITATFLYGYDPKTAGNLTKA

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	1.60 RPM
SRP017611_kidney	0.00 RPM	8.11 RPM
SRP017611_liver	0.00 RPM	18.88 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1564 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1564 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1564 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000695	1 retrocopy	retro_chof_37,
Oryctolagus cuniculus	ENSOCUG00000015538	2 retrocopies	retro_ocun_1564 , retro_ocun_436,
Tupaia belangeri	ENSTBEG00000004128	1 retrocopy	retro_tbel_198,
Vicugna pacos	ENSVPAG00000001029	1 retrocopy	retro_vpac_428,