RetrogeneDB ID: retro_ocun_102

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:91741123..91742020(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024057
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SLC25A4
• Ensembl ID: ENSOCUG00000002594
• Aliases: SLC25A4, SLC25A5
• Description: solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4 (SLC25A4), nuclear gene encoding mitochondrial protein, mRNA [Source:RefSeq mRNA;Acc:NM_001082686]

Sequence

>retro_ocun_102
ATGAGTGATCAGGCTTTGAGCTTCCTCAAGGACTTCCTGGCAGGTGGCGTCGCCGCTGCCGTCTCCAAGACTGCGGTCGC
CCCCATCGAGAGGGTCAAACTGCTGCTGCAGGTCCAGCATGCCAGCAAACAGATCAGCGCTGAGAAGCAGTACAAAGGGA
TCATTGATTGTGTGGTGAGGATCCCCAAGGAGCAGGGCTTTCTCTCCTTCTGGAGGGGTAACCTGGCCAACGTGATCCGG
TACTTCCCCACCCAAGCTCTCAACTTCGCCTTCAAGGACAAGTACAAGCAGATCTTCTTGGGGGGCGTGGATCGGCATAA
GCAGTTCTGGCGCTACTTCGCTGGTAACCTGGCCTCCGGTGGGGCAGCTGGGGCCACCTCCCTCTGCTTTGTCTACCCGC
TGGACTTTGCCAGGACCAGGTTGGCTGCCGACGTGGGCAAGGGTGCCGCCCAGCGTGAGTTCAGTGGTCTGGGCAACTGT
CTCACCAAGATCTTCAAGTCTGATGGCCTGAGGGGTCTCTACCAGGGTTTCAATGTCTCTGTGCAAGGCATCATTATCTA
CAGAGCTGCCTACTTCGGAGTCTATGATACTGCCAAGGGGATGTTGCCTGACCCCAAGAACGTGCACATTATCGTGAGCT
GGATGATCGCCCAGACTGTGACGGCAGTGGCCGGGCTGGTGTCCTACCCCTTTGACACTGTTCGTCGTAGGATGATGATG
CAGTCTGGCCGGAAAGGGGCTGACATTATGTACACGGGGACAGTTGACTGCTGGAAGAAGATTGCAAAAGATGAAGGAGC
CAAGGCTTTCTTCAAAGGTGCCTGGTCCAATGTGTTGAGAGGCATGGGTGGCGCTTTTGTATTGGTGTTGTATGATGAGA
TCAAAAAATATGTCTAA

Alignment

ORF - retro_ocun_102 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MSDQALSFLKDFLAGGVAAAVSKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSF
          MSDQALSFLKDFLAGGVAAAVSKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSF
Retrocopy MSDQALSFLKDFLAGGVAAAVSKTAVAPIERVKLLLQVQHASKQISAEKQYKGIIDCVVRIPKEQGFLSF

Parental  WRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFARTR
          WRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFARTR
Retrocopy WRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDRHKQFWRYFAGNLASGGAAGATSLCFVYPLDFARTR

Parental  LAADVGKGAAQREFSGLGNCLTKIFKSDGLRGLYQGFNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHI
          LAADVGKGAAQREFSGLGNCLTKIFKSDGLRGLYQGFNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHI
Retrocopy LAADVGKGAAQREFSGLGNCLTKIFKSDGLRGLYQGFNVSVQGIIIYRAAYFGVYDTAKGMLPDPKNVHI

Parental  IVSWMIAQTVTAVAGLVSYPFDTVRRRMMMQSGRKGADIMYTGTVDCWKKIAKDEGAKAFFKGAWSNVLR
          IVSWMIAQTVTAVAGLVSYPFDTVRRRMMMQSGRKGADIMYTGTVDCWKKIAKDEGAKAFFKGAWSNVLR
Retrocopy IVSWMIAQTVTAVAGLVSYPFDTVRRRMMMQSGRKGADIMYTGTVDCWKKIAKDEGAKAFFKGAWSNVLR

Parental  GMGGAFVLVLYDEIKKYV
          GMGGAFVLVLYDEIKKYV
Retrocopy GMGGAFVLVLYDEIKKYV

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	6.73 RPM	88.14 RPM
SRP017611_kidney	4.87 RPM	124.26 RPM
SRP017611_liver	2.70 RPM	25.82 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_102 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_102 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013208	1 retrocopy	retro_btau_1592,
Choloepus hoffmanni	ENSCHOG00000010542	3 retrocopies	retro_chof_1117, retro_chof_1777, retro_chof_807,
Dasypus novemcinctus	ENSDNOG00000007258	3 retrocopies	retro_dnov_1531, retro_dnov_1800, retro_dnov_390,
Dipodomys ordii	ENSDORG00000013787	1 retrocopy	retro_dord_268,
Erinaceus europaeus	ENSEEUG00000001021	2 retrocopies	retro_eeur_274, retro_eeur_36,
Macropus eugenii	ENSMEUG00000008508	4 retrocopies	retro_meug_222, retro_meug_549, retro_meug_6, retro_meug_921,
Microcebus murinus	ENSMICG00000010865	1 retrocopy	retro_mmur_1356,
Oryctolagus cuniculus	ENSOCUG00000002594	1 retrocopy	retro_ocun_102 ,
Oryctolagus cuniculus	ENSOCUG00000013268	11 retrocopies	retro_ocun_1002, retro_ocun_1233, retro_ocun_1457, retro_ocun_1694, retro_ocun_1705, retro_ocun_1862, retro_ocun_1877, retro_ocun_1890, retro_ocun_1932, retro_ocun_610, retro_ocun_708,
Ochotona princeps	ENSOPRG00000005957	6 retrocopies	retro_opri_1154, retro_opri_146, retro_opri_377, retro_opri_517, retro_opri_543, retro_opri_685,
Pan troglodytes	ENSPTRG00000016646	9 retrocopies	retro_ptro_146, retro_ptro_1588, retro_ptro_2143, retro_ptro_2364, retro_ptro_2388, retro_ptro_2517, retro_ptro_2525, retro_ptro_2819, retro_ptro_2882,
Pteropus vampyrus	ENSPVAG00000015279	1 retrocopy	retro_pvam_892,
Sarcophilus harrisii	ENSSHAG00000000932	1 retrocopy	retro_shar_160,
Tarsius syrichta	ENSTSYG00000004233	1 retrocopy	retro_tsyr_27,