RetrogeneDB ID: retro_ocun_1350

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:19753257..19753671(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3J
• Ensembl ID: ENSOCUG00000005376
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit J [Source:HGNC Symbol;Acc:3270]

Sequence

>retro_ocun_1350
CAGTTAGCAGATAATCTGTGGCTCAGGAAAGCACAGGGAGAGTCAGACCTTGAATTAGCAAAAAGAAATTTTTGGTATTA
ATAATATAGTTTCTGGAATAGATGCTATGAACCTGTCTTCAAGAGGTGATTTCAGAATTTGGGAAATTACTGAAAGGTAA
AATTATACAATATGCAAAGTAACTATATTCTGCCAGTATTTTGCAGACATTCTTAGTTCAGGATGTCTGTGTTTCATTGG
AAATGAGTGAGATTACCGATTTATTTACTGCACTTTACAGTGAAAATGGAAGCAAGCAAAACAAAGCCAAAAAGAAAGTG
TGGCCCCTGGAGGAGGATTAAAGGCTGACATGAAAGACAATCTGTAGATTATTGTGGTGAAGATGGAGGATATGTACATG
AGCAGGAAGACTTC

Alignment

ORF - retro_ocun_1350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.35 %
• Parental protein coverage: 55.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QLADKLRLKKLQEESDLELAK-ETFGVNNTVYGIDAMNPSSREDFTEFGKLLKDKITQYEKSLYYASFLE
          QLAD.L.L.K.Q.ESDLELAK.E.FG.NN.V.GIDAMN.SSR.DF...........T..........F..
Retrocopy QLADNLWLRKAQGESDLELAK>EIFGINNIVSGIDAMNLSSRGDFRIWEITER*NYTICKVTIFCQYFAD

Parental  AL-VRDVCISLEIDDLKKITNSLTVLCSE-KQKQEKQSKAKKKKKGVVPGGGLKATMKDDL-ADYGGYDG
          .L.V.DVC.SLE......IT...T.L.SE.K.KQ.KQS.....K..V.PGGGLKA.MKD.L..DY.G.DG
Retrocopy IL>VQDVCVSLE---MSEITDLFTALYSE<KWKQAKQS----QKESVAPGGGLKADMKDNL<VDYCGEDG

Parental  GYAQDYEDF
          GY....EDF
Retrocopy GYVHEQEDF

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	25.66 RPM
SRP017611_kidney	0.00 RPM	28.48 RPM
SRP017611_liver	0.08 RPM	16.03 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1350 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1350 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1350 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002412	1 retrocopy	retro_cjac_589,
Cavia porcellus	ENSCPOG00000012396	3 retrocopies	retro_cpor_1357, retro_cpor_1358, retro_cpor_500,
Gorilla gorilla	ENSGGOG00000000548	2 retrocopies	retro_ggor_1687, retro_ggor_41,
Macropus eugenii	ENSMEUG00000010372	1 retrocopy	retro_meug_256,
Monodelphis domestica	ENSMODG00000017696	1 retrocopy	retro_mdom_141,
Mus musculus	ENSMUSG00000027236	1 retrocopy	retro_mmus_18,
Nomascus leucogenys	ENSNLEG00000005568	1 retrocopy	retro_nleu_2848,
Oryctolagus cuniculus	ENSOCUG00000005376	1 retrocopy	retro_ocun_1350 ,