RetrogeneDB ID: retro_ocun_333

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:5987361..5988105(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUFM
• Ensembl ID: ENSOCUG00000002683
• Aliases: None
• Description: Tu translation elongation factor, mitochondrial [Source:HGNC Symbol;Acc:12420]

Sequence

>retro_ocun_333
GAGTTAGGCTACAAAGGGGAGGAGGCCCCTGTCATCGTGGGCTCTGCCATCTGTGCCCTGGAGCAATGGGACACCGAGCT
CGGCGTGAAGTCGGTGCAGAAGCTGCTGGACGCCGTGGACACCTACATCCCGGTGCCCACCCGCGACCTGGAGAAGCCTT
TCCTGCTGCCCGTCGAGTCTGTCTACTCGATCCCGGGCCGGGGCACAGTGGTGACAGGGACGCTAGAGCGCGGCATCTTG
AAGAAGGGAGACCAGTGCGAGTTCCTCGGCCACAGCAAGAACATCCGCACGGTGGTGACAGGCATTGAGATGTCCCACAA
GAGCCTGGAGAGGGCCGAGGCCGGGGACAACCTGGGGGCCCTGGTCCGAGGCTTGAAGCGGGAGGACCTGAGGCGCGGCT
TGGTCATGGCCAAGCCGGGCTCCATCCAGCCCCACCAGAAGGTGGAGGCGCAGGTTTACATCCTCAGCAAGGAGGAGGGC
GGCCGCCACAAACCCTTCGTGTCCCACTTCATGCCCGTCATGTTCTCCCTGACCTGGGACATGGCCTGCCGGGTGCTCCT
GCCCCCAGGGAAGGAGCTGGCCATGCCCGGGGAGGACCTGAAGCTCAGCCTAATCCTGCGACAGCCAATGATCGTAGAGA
AAGGCCAGCGTTTCACCCTGCGGGACGGCAACTGCACCATCGGCACAGGCCTCCTCACAGACACGCCCGCCATGACCGAG
GAGGACAAGAGCATCAAGTGGAGC

Alignment

ORF - retro_ocun_333 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.97 %
• Parental protein coverage: 54.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EFGYKGEEAPVIVGSALCALEQRDPELGVKSVQKLLDAVDTYIPVPTRDLEKPFLLPVESVYSIPGRGTV
          E.GYKGEEAPVIVGSA.CALEQ.D.ELGVKSVQKLLDAVDTYIPVPTRDLEKPFLLPVESVYSIPGRGTV
Retrocopy ELGYKGEEAPVIVGSAICALEQWDTELGVKSVQKLLDAVDTYIPVPTRDLEKPFLLPVESVYSIPGRGTV

Parental  VTGTLERGILKKGDECEFLGHSKNIRTVVTGIEMFHKSLERAEAGDNLGALVRGLKREDLRRGLVMAKPG
          VTGTLERGILKKGD.CEFLGHSKNIRTVVTGIEM.HKSLERAEAGDNLGALVRGLKREDLRRGLVMAKPG
Retrocopy VTGTLERGILKKGDQCEFLGHSKNIRTVVTGIEMSHKSLERAEAGDNLGALVRGLKREDLRRGLVMAKPG

Parental  SIQPHQKVEAQVYILSKEEGGRHKPFVSHFMPVMFSLTWDMACRVLLPPGKELAMPGEDLKLSLILRQPM
          SIQPHQKVEAQVYILSKEEGGRHKPFVSHFMPVMFSLTWDMACRVLLPPGKELAMPGEDLKLSLILRQPM
Retrocopy SIQPHQKVEAQVYILSKEEGGRHKPFVSHFMPVMFSLTWDMACRVLLPPGKELAMPGEDLKLSLILRQPM

Parental  ILEKGQRFTLRDGNRTIGTGLVTDTPAMTEEDKNIKWS
          I.EKGQRFTLRDGN.TIGTGL.TDTPAMTEEDK.IKWS
Retrocopy IVEKGQRFTLRDGNCTIGTGLLTDTPAMTEEDKSIKWS

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	0.99 RPM	73.62 RPM
SRP017611_kidney	3.04 RPM	128.42 RPM
SRP017611_liver	1.00 RPM	45.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_333 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_333 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016474	1 retrocopy	retro_dord_278,
Homo sapiens	ENSG00000178952	1 retrocopy	retro_hsap_1816,
Macropus eugenii	ENSMEUG00000011131	1 retrocopy	retro_meug_1783,
Monodelphis domestica	ENSMODG00000015564	1 retrocopy	retro_mdom_384,
Mus musculus	ENSMUSG00000073838	1 retrocopy	retro_mmus_10,
Ornithorhynchus anatinus	ENSOANG00000013114	1 retrocopy	retro_oana_36,
Oryctolagus cuniculus	ENSOCUG00000002683	1 retrocopy	retro_ocun_333 ,
Pan troglodytes	ENSPTRG00000007939	1 retrocopy	retro_ptro_1174,
Rattus norvegicus	ENSRNOG00000018604	1 retrocopy	retro_rnor_1134,
Vicugna pacos	ENSVPAG00000009541	1 retrocopy	retro_vpac_346,
Drosophila melanogaster	FBgn0033184	1 retrocopy	retro_dmel_52,