RetrogeneDB ID: retro_ocun_379

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:88933554..88934467(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024262
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AASDHPPT
• Ensembl ID: ENSOCUG00000000231
• Aliases: None
• Description: aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase [Source:HGNC Symbol;Acc:14235]

Sequence

>retro_ocun_379
ATGGTTTTCCCCGCCAAGCGGCTGTGCTTGGTGCCATCCATGGAGGGCGTCCGCTGTGGCACCTGGCTGCCGAGTTGAGC
CAAATGGCTGCTGGCGGTGCGGTCGATCCAGCCTGAGGAGAAGGAGCGCATTGGCCAGTTCGTCTTTGCCCGGGGCGCTA
AGGCAGCCTTGGCTGGTCTTCTGATGATAAGGAAATTAGTTGCAGAGAAATTGAATATCCCTTGGAATAATATTCGTTTG
CAAAGAACTGCAAAAGGAAAATCAGTTCTTGCAAAGGACTCATTGAATCCTTACCCCAATTTCAACTTTAACATCTCATC
AAGGGGACTTTGCGGTACTTGCTGCTGAACCTGAACTACAAGTTGGAGTCCATATAATGAAGACTAGTTTTCCAGGTCGC
GGTTCAATTCCAGAATTCTTTCATATTATGAAAAGGAAGTTTACCAACAAGGAATGGGAAACCATCAGAAGCTTTAAGGA
TGAATGGACTCAGCTGGATATGTTTTATAGGAATTGGGCATTGAAAGAAAACTACATAAAAGTCATTGGTGTTGGACTAG
GATTTGAATTACAGCGGCTTGAATTTGAAATATCTCCCTTAAACTTGGATATAGGCCAAGTTTATAAAGAAACACGTTTG
TTCCTGGATGGTGAAGAAGAAAAAGAGTGGGCATTTGAGGAAAGCAAAATAGATGAACATCATTTTGTTGCAGTAGCTAT
TAGGAAACCCGATGGATCTAGACATCAAGATGTTCCATCTCTAGATGATTCTAAACCAACCCAGAGGCAGTTTACTATTC
TCACCTTTAATGATTTAATATCATCTGCTGTTCCTATGACACCTGAAGATCCTTCATTTTGGGACTGTTTTTGTTTCACA
GAAGAAATTCCAATACGAAATGGTACAAAGTCA

Alignment

ORF - retro_ocun_379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVFPAKRLCLVPSMEGVRWAFSCGTWLPSRAEWLLAVRSIQPEEKERIGQFVFARDAKAAMAGRLMIRKL
          MVFPAKRLCLVPSMEGVR....CGTWLPS.A.WLLAVRSIQPEEKERIGQFVFAR.AKAA.AG.LMIRKL
Retrocopy MVFPAKRLCLVPSMEGVR----CGTWLPS*AKWLLAVRSIQPEEKERIGQFVFARGAKAALAGLLMIRKL

Parental  VAEKLNIPWNNIRLQRTAKGKPVLA-KDSLNPYPNFNF-NISHQGDFAVLAAEPELQVGVDIMKTSFPGR
          VAEKLNIPWNNIRLQRTAKGK.VLA.K......P.F.....SHQGDFAVLAAEPELQVGV.IMKTSFPGR
Retrocopy VAEKLNIPWNNIRLQRTAKGKSVLA<KGLIESLPQFQL<LTSHQGDFAVLAAEPELQVGVHIMKTSFPGR

Parental  GSIPEFFHIMKRKFTNKEWETIRSFKDEWTQLDMFYRNWALKESYIKAIGVGLGFELQRLEFEISPLNLD
          GSIPEFFHIMKRKFTNKEWETIRSFKDEWTQLDMFYRNWALKE.YIK.IGVGLGFELQRLEFEISPLNLD
Retrocopy GSIPEFFHIMKRKFTNKEWETIRSFKDEWTQLDMFYRNWALKENYIKVIGVGLGFELQRLEFEISPLNLD

Parental  IGQVYKETRLFLDGEEEKEWAFEESKIDEHHFVAVALRKPDGSRHQDVPSLDDSKPSQRQFTILTFNDLI
          IGQVYKETRLFLDGEEEKEWAFEESKIDEHHFVAVA.RKPDGSRHQDVPSLDDSKP.QRQFTILTFNDLI
Retrocopy IGQVYKETRLFLDGEEEKEWAFEESKIDEHHFVAVAIRKPDGSRHQDVPSLDDSKPTQRQFTILTFNDLI

Parental  SSAVPMTPEDPSFWDCFCFTEEIPIRNGTKS
          SSAVPMTPEDPSFWDCFCFTEEIPIRNGTKS
Retrocopy SSAVPMTPEDPSFWDCFCFTEEIPIRNGTKS

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	22.85 RPM
SRP017611_kidney	0.00 RPM	8.01 RPM
SRP017611_liver	0.00 RPM	5.16 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_379 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_379 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012279	1 retrocopy	retro_btau_134,
Echinops telfairi	ENSETEG00000004248	2 retrocopies	retro_etel_1231, retro_etel_1503,
Myotis lucifugus	ENSMLUG00000016238	4 retrocopies	retro_mluc_1361, retro_mluc_1362, retro_mluc_1363, retro_mluc_479,
Mus musculus	ENSMUSG00000025894	1 retrocopy	retro_mmus_2827,
Oryctolagus cuniculus	ENSOCUG00000000231	1 retrocopy	retro_ocun_379 ,
Ictidomys tridecemlineatus	ENSSTOG00000000268	1 retrocopy	retro_itri_1438,
Tarsius syrichta	ENSTSYG00000005102	1 retrocopy	retro_tsyr_338,