RetrogeneDB ID: retro_ocun_369

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:59818469..59819246(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026530
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EEF1G
• Ensembl ID: ENSOCUG00000020959
• Aliases: None
• Description: eukaryotic translation elongation factor 1 gamma (EEF1G), mRNA [Source:RefSeq mRNA;Acc:NM_001101703]

Sequence

>retro_ocun_369
GCTTACTTGAAGACGAGGACTTTCCTGGTGGGCGAGCGAGTGACACTGGCTGACATCACAGTTGTCTGCACCCTTTTATG
GTTCTATAAACAGGTCTTGGAGGCTTCTTTCCACCAGGCTTTTCCGAATACCAACCACTGGTTCCTCACCTGCATTAATC
AGCTGCAGTTTCGGGCTGTCTTGGGGGAGATGAAACTGTGTGAAAAGATGGCCCATTTTGATGCTAAAAAGTTTGCAGAG
AGCCAGCCTAAAAAGGACACGCCACGGAAAGAGCAAGGCTCACAGGAGGAGAAGCAGAAGCCCCAGACTGAGCGGAAAGA
GGAGAAAAGGGCAGCTGCCCCAGCTCCTGATCAAGAGATGGACGAATGCGAGCAGGCACTGGCTGCTGAGCCCAAGGCAA
AGGACCCCTTTGCCCACCTGCCCAAAAGTACCTTTGTGTTGGATGAGTTTAAGCACAAGTGCTCCAATGAGGATACTCTC
TCTGTGGCTCTGCCATATTTTTGGGAGCACTTTGACAAGGATGGCTGGTCTTTGTGGTATGCTGAGCACCGTTTCTCTGA
AGAGCTCACGCAGACTTTCATGAGTTGCAACCTCATCACTGGAATGTTCCAGCGGTTGGATAAGCTGAGGAAGAATGCCT
TTGCCAGTGTCATCCTCTTTGGAACCAACAATAGCAGCTCCATTTCTGGAATATGGGTCTTCCGAGGCCAAGAGCTTGCC
TTTCCGCTGAGTCCAGATTGGCAGGTGGACTACGAGTCGTGTACGTGGAGGAAACTG

Alignment

ORF - retro_ocun_369 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.66 %
• Parental protein coverage: 64.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AHLKTRTFLVGERVTLADITVVCTLLWLYKQVLEPSFRQAFPNTNRWFLTCINQPQFRAVLGEVKLCEKM
          A.LKTRTFLVGERVTLADITVVCTLLW.YKQVLE.SF.QAFPNTN.WFLTCINQ.QFRAVLGE.KLCEKM
Retrocopy AYLKTRTFLVGERVTLADITVVCTLLWFYKQVLEASFHQAFPNTNHWFLTCINQLQFRAVLGEMKLCEKM

Parental  AQFDAKKFAESQPKKDTPRKEKGSREEKQKPQAERKEEKKAAAPAPEEEMDECEQALAAEPKAKDPFAHL
          A.FDAKKFAESQPKKDTPRKE.GS.EEKQKPQ.ERKEEK.AAAPAP..EMDECEQALAAEPKAKDPFAHL
Retrocopy AHFDAKKFAESQPKKDTPRKEQGSQEEKQKPQTERKEEKRAAAPAPDQEMDECEQALAAEPKAKDPFAHL

Parental  PKSTFVLDEFKRKYSNEDTLSVALPYFWEHFDKDGWSLWYAEYRFPEELTQTFMSCNLITGMFQRLDKLR
          PKSTFVLDEFK.K.SNEDTLSVALPYFWEHFDKDGWSLWYAE.RF.EELTQTFMSCNLITGMFQRLDKLR
Retrocopy PKSTFVLDEFKHKCSNEDTLSVALPYFWEHFDKDGWSLWYAEHRFSEELTQTFMSCNLITGMFQRLDKLR

Parental  KNAFASVILFGTNNSSSISGIWVFRGQELAFPLSPDWQVDYESYTWRKL
          KNAFASVILFGTNNSSSISGIWVFRGQELAFPLSPDWQVDYES.TWRKL
Retrocopy KNAFASVILFGTNNSSSISGIWVFRGQELAFPLSPDWQVDYESCTWRKL

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	128.75 RPM
SRP017611_kidney	0.20 RPM	215.69 RPM
SRP017611_liver	0.00 RPM	53.41 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_369 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_369 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_369 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006745	1 retrocopy	retro_amel_772,
Canis familiaris	ENSCAFG00000015834	6 retrocopies	retro_cfam_1241, retro_cfam_1398, retro_cfam_1862, retro_cfam_478, retro_cfam_638, retro_cfam_653,
Callithrix jacchus	ENSCJAG00000018949	6 retrocopies	retro_cjac_1464, retro_cjac_1770, retro_cjac_1942, retro_cjac_3147, retro_cjac_841, retro_cjac_874,
Equus caballus	ENSECAG00000014334	1 retrocopy	retro_ecab_419,
Latimeria chalumnae	ENSLACG00000014700	1 retrocopy	retro_lcha_82,
Loxodonta africana	ENSLAFG00000003339	1 retrocopy	retro_lafr_381,
Monodelphis domestica	ENSMODG00000007691	1 retrocopy	retro_mdom_68,
Mustela putorius furo	ENSMPUG00000013942	2 retrocopies	retro_mputfur_427, retro_mputfur_944,
Nomascus leucogenys	ENSNLEG00000003528	2 retrocopies	retro_nleu_1510, retro_nleu_681,
Oryctolagus cuniculus	ENSOCUG00000020959	3 retrocopies	retro_ocun_1693, retro_ocun_369 , retro_ocun_693,
Pongo abelii	ENSPPYG00000029434	5 retrocopies	retro_pabe_2237, retro_pabe_2378, retro_pabe_2409, retro_pabe_2473, retro_pabe_3690,
Pan troglodytes	ENSPTRG00000003768	3 retrocopies	retro_ptro_1879, retro_ptro_2017, retro_ptro_3159,
Rattus norvegicus	ENSRNOG00000020075	8 retrocopies	retro_rnor_1312, retro_rnor_2126, retro_rnor_2235, retro_rnor_2269, retro_rnor_2468, retro_rnor_2617, retro_rnor_2928, retro_rnor_979,
Sorex araneus	ENSSARG00000011232	1 retrocopy	retro_sara_718,