RetrogeneDB ID: retro_ocun_738

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:13316939..13317509(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000022847
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEC11C
• Ensembl ID: ENSOCUG00000009204
• Aliases: None
• Description: SEC11 homolog C (S. cerevisiae) [Source:HGNC Symbol;Acc:23400]

Sequence

>retro_ocun_738
ATGAGAAAGTGTGGGGGTCGGAGACTCCCGGAGCCAGCGTCCGGCCTGGACATCTTCGGGGACCTGAGAAAGGTGAACAA
GCGCCAGCTCTATTACCAGGTTTTAAACTTGGCCATGATCGTGTCTTCCGCACTCATAACCTGGAAAGGCTTGATCGTCC
TCACCGGCAGCGAGAGCCCCATCGTGGTGGTGGTGCTGAGTGGCAGCACGGAGCCAGCCTTTCACAGGGGAGACCTCCTG
TTCCTCACAAAAGACCTGATCAGAGCCGGGGAAATCGCTGTTTTTAAAGTGGAAGGACGAGACATTCCAATAGTTCACAG
AGTAATCAAAGTTCACGAAAAAGATAATGGAGACATCAAATTTCTGACTAAAGGAGATAATAATGAAGTTGACGACAGAG
GATTGCACAAAGAAAGCCAGAACTGACTCGAGAAGAAGGATGTGGTGGGAAGAGCAAGAGGGTTTTTGCCGTATGTTGGC
TTGGTCACCATAATAATGAATGACTATCCAAAGTTCAAGTGCGCCCTTCTGGCTGTGATGGGTGCATGTGTGTTACTAAA
ACGTGAATCC

Alignment

ORF - retro_ocun_738 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.53 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGRAGGVAAHLPASGLDIFGDLRKMNKRQLYYQVLNFAMIVSSALMIWKGLIVLTGSESPIVVV-LSGSM
          M...GG.....PASGLDIFGDLRK.NKRQLYYQVLN.AMIVSSAL..WKGLIVLTGSESPIVVV.LSGS.
Retrocopy MRKCGGRRLPEPASGLDIFGDLRKVNKRQLYYQVLNLAMIVSSALITWKGLIVLTGSESPIVVVVLSGST

Parental  EPAFHRGDLLFLTNFREDPIRAGEIVVFKVEGRDIPIVHRVIKVHEKDNGDIKFLTKGDNNEVDDRGLYK
          EPAFHRGDLLFLT....D.IRAGEI.VFKVEGRDIPIVHRVIKVHEKDNGDIKFLTKGDNNEVDDRGL.K
Retrocopy EPAFHRGDLLFLT---KDLIRAGEIAVFKVEGRDIPIVHRVIKVHEKDNGDIKFLTKGDNNEVDDRGLHK

Parental  EGQNWLEKKDVVGRARGFLPYVGMVTIIMNDYPKFKYALLAVMGAYVLLKRES
          E.QN.LEKKDVVGRARGFLPYVG.VTIIMNDYPKFK.ALLAVMGA.VLLKRES
Retrocopy ESQN*LEKKDVVGRARGFLPYVGLVTIIMNDYPKFKCALLAVMGACVLLKRES

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	0.06 RPM	74.67 RPM
SRP017611_kidney	0.00 RPM	75.71 RPM
SRP017611_liver	0.08 RPM	49.79 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_738 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_738 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_738 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000017024	3 retrocopies	retro_ecab_1009, retro_ecab_455, retro_ecab_989,
Echinops telfairi	ENSETEG00000005115	2 retrocopies	retro_etel_1081, retro_etel_1139,
Felis catus	ENSFCAG00000006501	1 retrocopy	retro_fcat_1815,
Microcebus murinus	ENSMICG00000016052	1 retrocopy	retro_mmur_271,
Monodelphis domestica	ENSMODG00000020427	2 retrocopies	retro_mdom_1517, retro_mdom_377,
Oryctolagus cuniculus	ENSOCUG00000008205	1 retrocopy	retro_ocun_849,
Oryctolagus cuniculus	ENSOCUG00000009204	2 retrocopies	retro_ocun_738 , retro_ocun_895,
Otolemur garnettii	ENSOGAG00000002570	1 retrocopy	retro_ogar_400,
Pteropus vampyrus	ENSPVAG00000002950	2 retrocopies	retro_pvam_620, retro_pvam_869,
Sus scrofa	ENSSSCG00000004912	1 retrocopy	retro_sscr_775,
Tupaia belangeri	ENSTBEG00000014804	1 retrocopy	retro_tbel_2357,
Tursiops truncatus	ENSTTRG00000007676	5 retrocopies	retro_ttru_1278, retro_ttru_1508, retro_ttru_1780, retro_ttru_1916, retro_ttru_490,