RetrogeneDB ID: retro_ocun_1440

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:27059081..27059515(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL5
• Ensembl ID: ENSOCUG00000010405
• Aliases: None
• Description: methyltransferase like 5 [Source:HGNC Symbol;Acc:25006]

Sequence

>retro_ocun_1440
GTACTTAGCATGAGAACTGCTTTTTTAGGAGCAGGACTTTGTGTTGGATTTAACATAAATGACAATGCATTGGAAATGAA
ATGAAAAAGCTTGAATTAACAAATGTTGATGCAGTTCAATGTGATATGTGATATGTGCACATTATCTAAAAAAATATCTA
AGTCATTTTATATAGCAATTATGAATCCTCCCTTTGGCACCAAAACCAATAAAGGACAGATATGGCTTTTCTGAAGACTG
CTTTGGAAAGGGCAAGAATAGCAATATACTCCTTAAACAAAACCTCAGCTACAGAACATGTTAGAAAGAAAGCTGAAAAA
TGGAAAATCAGTATAGATGTAATTACAGAGCTTTGATATGACCTGTCAGCATCCTACAACTTTTATAAAAAGCAACCAGC
GGACACTGATGAGTCCCTAATTTGGTTTTCTTTT

Alignment

ORF - retro_ocun_1440 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.86 %
• Parental protein coverage: 69.86 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLSIGTAMLGAGLCVGFDIDEDALEIFNRNVEEFELTNVDMVQCDVCTLPNRMPKSFDTVIMNPPFGTKK
          VLS..TA.LGAGLCVGF.I...ALE..........L.......CD.CTL.....KSF...IMNPPFGTK.
Retrocopy VLSMRTAFLGAGLCVGFNINDNALEMK*KSLN*QMLMQFNVI-CDMCTLSKKISKSFYIAIMNPPFGTKT

Parental  NKG-TDMAFLKTALEMARTAVYSLHKSSTREHIQKKAAEWKIKIDVIAELRYDLPASYNFHKKQSVDIEV
          NKG.TDMAFLKTALE.AR.A.YSL.K.S..EH..KKA..WKI.IDVI.EL.YDL.ASYNF.KKQ..D...
Retrocopy NKG<TDMAFLKTALERARIAIYSLNKTSATEHVRKKAEKWKISIDVITEL*YDLSASYNFYKKQPADTDE

Parental  DLVRFSF
          .L..FSF
Retrocopy SLIWFSF

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	6.18 RPM
SRP017611_kidney	0.00 RPM	12.97 RPM
SRP017611_liver	0.00 RPM	4.70 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1440 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1440 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1440 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003343	1 retrocopy	retro_cpor_373,
Dasypus novemcinctus	ENSDNOG00000013460	2 retrocopies	retro_dnov_1043, retro_dnov_773,
Homo sapiens	ENSG00000138382	2 retrocopies	retro_hsap_1365, retro_hsap_2930,
Gorilla gorilla	ENSGGOG00000022484	2 retrocopies	retro_ggor_1064, retro_ggor_2032,
Loxodonta africana	ENSLAFG00000018044	2 retrocopies	retro_lafr_1213, retro_lafr_864,
Macaca mulatta	ENSMMUG00000023054	3 retrocopies	retro_mmul_1430, retro_mmul_1953, retro_mmul_2193,
Nomascus leucogenys	ENSNLEG00000005018	4 retrocopies	retro_nleu_1070, retro_nleu_1919, retro_nleu_753, retro_nleu_990,
Oryctolagus cuniculus	ENSOCUG00000010405	1 retrocopy	retro_ocun_1440 ,
Pongo abelii	ENSPPYG00000012916	2 retrocopies	retro_pabe_2281, retro_pabe_2523,
Pan troglodytes	ENSPTRG00000012621	3 retrocopies	retro_ptro_1822, retro_ptro_2062, retro_ptro_938,