RetrogeneDB ID: retro_ocun_863

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:31963760..31964573(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6AP1
• Ensembl ID: ENSOCUG00000017631
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal accessory protein 1 (ATP6AP1), mRNA [Source:RefSeq mRNA;Acc:NM_001171377]

Sequence

>retro_ocun_863
GACCGAACCCCTTCCTCCCTGATGCTTCCCGCCCTCGACTGCTGTGCGGTCGCCACTCTGACGGCCTACCTGCAGGAGAA
ACTAGAGACCAGCGCCTGGCCCGTGGACTTGGCCACCCTATGAGAGCTGAAGCTCAATGCCAGCCTCCCCACCCTGCTGC
TCATCCACCTGCCCTACATGGCCAGTTCCGGTCCAGTAGCACCCAGGGAAGTCCTTACAGGCAACGATGAAGTCATCAGG
CAGGTGCTGAGCAAACTCAACTCTGAGGACATTCCCTATACAGCAGGCTTCACAGTGGCCCACCCTTCCAGGATGGGCCG
TGATGTAGCTGTGGTGGCCCGGGAACTAGGTCGCCAGCTGCTACAGAAACAGCCAGTGTCAGCTGTCATCCATCCCCCTG
TGAGTTACAACGACACTGCTCCCCGGATCCTGTTCTGGGCCCAAAACTTCTCTGTGGCCTACAAGGACCAGTGGGAAGAC
CTGACATCCCTCACCTTTGGGGTGCAGGAGCTCAACCTGACTGACTCCTTGAATGACTCCATTGCCAGGCTCTCGCTGAC
CTACGAACAACTCTTTGGTACCATGGTGACATTCAAGTTCATTCTGGCTAACCGCTTCTACCCCATGTCTGCCAAGAACT
GGTTTACCATGGAGTGCCTGGAAATCCACAGCAACGGCTCTGTTGTCTACTTCAACGCTTCCCAGGTGACAGGGCCCAGC
ATCTACTCCTTGCATTGCAAGTATGTGAGCAGTCTGAGCAACAAGGGCAATCTCCTGGTGGCCCGCCCACAGCCCTCACT
GTGGCACGTGACT

Alignment

ORF - retro_ocun_863 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.84 %
• Parental protein coverage: 57.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLAPSSLVLPAVDWYAVSTLTTYLQEKLGASPLHVDLATLRELKLNASLPALLLIRLPYTTRYGLMAPRE
          D..PSSL.LPA.D..AV.TLT.YLQEKL..S...VDLATL.ELKLNASLP.LLLI.LPY....G..APRE
Retrocopy DRTPSSLMLPALDCCAVATLTAYLQEKLETSAWPVDLATL*ELKLNASLPTLLLIHLPYMASSGPVAPRE

Parental  VLTGNDEVIGQVLSTLQSEDVPYTAALTAVRPSRVARDVAMVAGGLGRQLLQKQPVSTVIHPPVSYNTTV
          VLTGNDEVI.QVLS.L.SED.PYTA..T...PSR..RDVA.VA..LGRQLLQKQPVS.VIHPPVSYN.T.
Retrocopy VLTGNDEVIRQVLSKLNSEDIPYTAGFTVAHPSRMGRDVAVVARELGRQLLQKQPVSAVIHPPVSYNDTA

Parental  PRILFWAQNFSVAYKDQWEDLTPLTFGVQELNLTGSFWSDSIAWLSLTYDHLFGTTVTFKFVLANRFYPV
          PRILFWAQNFSVAYKDQWEDLT.LTFGVQELNLT.S...DSIA.LSLTY..LFGT.VTFKF.LANRFYP.
Retrocopy PRILFWAQNFSVAYKDQWEDLTSLTFGVQELNLTDSL-NDSIARLSLTYEQLFGTMVTFKFILANRFYPM

Parental  SARHWFTMERLEIHGNGSVVYFNASQVTGPSIYSFHCEYVSSLAQDGSLLVARTQPSLWQMT
          SA..WFTME.LEIH.NGSVVYFNASQVTGPSIYS.HC.YVSSL...G.LLVAR.QPSLW..T
Retrocopy SAKNWFTMECLEIHSNGSVVYFNASQVTGPSIYSLHCKYVSSLSNKGNLLVARPQPSLWHVT

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	257.84 RPM
SRP017611_kidney	0.00 RPM	157.61 RPM
SRP017611_liver	0.00 RPM	28.21 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_863 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_863 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_863 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000008869	1 retrocopy	retro_mdom_1068,
Mus musculus	ENSMUSG00000019087	1 retrocopy	retro_mmus_1198,
Oryctolagus cuniculus	ENSOCUG00000017631	1 retrocopy	retro_ocun_863 ,
Sarcophilus harrisii	ENSSHAG00000005317	1 retrocopy	retro_shar_519,