RetrogeneDB ID: retro_ocun_1611

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018717:375275..375710(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS29
• Ensembl ID: ENSOCUG00000011924
• Aliases: None
• Description: vacuolar protein sorting 29 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14340]

Sequence

>retro_ocun_1611
CACATTCTCTGGACTGCACACTTCTGCTCCAAATAAAGCACTGACTCTCTGCGGACTCTGGCTGCTGTTGTTCACATGTG
AGAGGAGACGTTGATGAGAATCTGAATGATACAGAACAGGAAGATGTGACTGTCGACGGTGCAAAATTGGCTTGACCCGT
GGACTTCGAGTCTTTCCGTGGGGCGGTCCTGCCAGCTTCGCCCAGCGGCAGAGCCTGCTTGATGTGGACATTCTTATCTC
ATCATTCAACGTGCACACAATTTGAAGCATTTGAGCATGAAAACAAATTCTAGATTAGCCCAGGTTCTGCCACTGGGGCG
TATAATGTCTTGGAAAGAAACATTGTTCCTTCATTCGTGTTGATGGGTAGCCAGGCTTCCCCAGTGGTCACTTAATGAGT
TTCAGCTAACTGGAGATGACGATAGAACACAAAAA

Alignment

ORF - retro_ocun_1611 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.4 %
• Parental protein coverage: 81.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HILCTGNLCTKESYDYLKTLAGDVHI-VRGDFDENLNYPEQKVVTVG-QFKIGLIHGHQVIPWGDMASLA
          HIL.T...C.K.S.D.L.TLA..VH..VRGD.DENLN..EQ..VTV....KIGL..G..V.PWG..AS.A
Retrocopy HILWTAHFCSK*STDSLRTLAAVVHM<VRGDVDENLNDTEQEDVTVD<RCKIGLTRGLRVFPWGGPASFA

Parental  LLQRQFDVDILISG-HTH-KFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVT-YVYQL
          ..Q...DVDILIS....H..FEAFEHENKF.I.PGSATGAYN.LE.NI.PSFVLM..QAS.VVT....QL
Retrocopy QRQSLLDVDILISSFNVH>QFEAFEHENKF*ISPGSATGAYNVLERNIVPSFVLMGSQASPVVT>NEFQL

Parental  IGDDVKVER
          .GDD.....
Retrocopy TGDDDRTQK

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	0.22 RPM	83.78 RPM
SRP017611_kidney	0.41 RPM	47.13 RPM
SRP017611_liver	0.00 RPM	16.49 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1611 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1611 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1611 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000001891	1 retrocopy	retro_acar_30,
Felis catus	ENSFCAG00000004135	2 retrocopies	retro_fcat_165, retro_fcat_848,
Loxodonta africana	ENSLAFG00000006176	1 retrocopy	retro_lafr_1115,
Oryctolagus cuniculus	ENSOCUG00000011924	1 retrocopy	retro_ocun_1611 ,
Tupaia belangeri	ENSTBEG00000012756	4 retrocopies	retro_tbel_1121, retro_tbel_2187, retro_tbel_330, retro_tbel_4424,
Tursiops truncatus	ENSTTRG00000015090	2 retrocopies	retro_ttru_1404, retro_ttru_1492,