RetrogeneDB ID: retro_ocun_1593

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018706:3885557..3886837(-)
• Located in intron of: ENSOCUG00000013399

Retrocopy information

• Ensembl ID: ENSOCUG00000017406
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EXOC5
• Ensembl ID: ENSOCUG00000000756
• Aliases: None
• Description: exocyst complex component 5 [Source:HGNC Symbol;Acc:10696]

Sequence

>retro_ocun_1593
AAATTGCAAGGTTTTGTGAAAGACCAGTTAGAAGAATGTAGGAAATCTGATGCAGAGCAGTATCTCAAAAACCTCTATGA
TCTATATACAAGAACCACCAATCTTTCCAGCAAGTTGATGGAGTTTAATTTGGGTACTGATAAACAGACTTTCTTGTCCA
AGCTTATCAAATCCATTTTCATTTCCTATTTGGAAGACTATATTGAAGTGGAGACTGGATATCTGAAAAGCAGAAGTGGT
ATGATCCTACAGCGTTATTATGATTCAAAAAATCATCAAAAGAGATCCATTGGCACAGGAGGTATTCAGGATTTGAAAGA
GAGAATTAGACAACGTACCAACTTACCACTGGGGCCAAGTATTGATACCCATGGGGAAACTTTCCTATCCCAAGAAGTGG
TGGTTAATCTTTTACAAGAAACCAAACAAGCCTTTGAAAGATGTCATAGGCTCTCTGATCCCTCTGATTTACCAAGGAAT
GCCTTTAGAATTTTTACCATTCTTGTGGAATTTTTATGTATTGAGCATATTGATTATGCTTTGGAAACAGGACTTGCCGG
AATTCCTTCTTCAGATTCTAGGAATGCAAATCTGTATTTTTTGGATGTTGTGCAACAAGCCAATACTATTTTTCATCTTT
TTGACAAGCAGTTTAATGATCACCTTATGCCACTAATAAGCTCTTCTCCTAAGTTATCTGAATGCCTTCAGAAGAGAAAA
GAAATAATTGAACAAATGGAGATGAAATTGGATACTGGTATTGATAGGACATTAAATTGTATGATTGGACAGATGAAGCT
TATATCTTGGCTGCAGAACAAAAGAAAACAGATTTTAAGCCAGAGGATGAAAACAATGTTTTGATTCAATATACTAATGC
CTGTGTAAAAGTCTGTGCTTATGTAAGAAAACAAGTAGAAAAGATAAAAAATTCCATGGATGGAAAGAATGTAGACACAG
TTTTGATGGAACTTGGAGTACGTTTTCATCGACTTATTTATGAACATCTTCAACAATATTCCTACAGTTGTATGGGTGGC
ATGTTAGCAATTTGTGATGTAGCTGAATATAGAAAGTGTGCCAAAGACTTCAAGATTCCAATGGTATTACATCTTTTTGA
TACTCTGCATGCACTTTGCAATCTTCTGGTAGTTGCCCCAGATAATTTAAAGCAAGTCTGCTCAGGAGAACAGCTTGCTA
ACCTGGACAAGAACATACTTCACTCCTTTGTACAACTTTGCGCTGACTATAGATCTGCCCGCCTAGCTCGACACTTCAGC

Alignment

ORF - retro_ocun_1593 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.97 %
• Parental protein coverage: 61. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLQGFVKDQLEECRKSDAEQYLKNLYDLYTRRTTNLSSKLMEFNLGTDKQTFLSKLIKSIFISYLENYIE
          KLQGFVKDQLEECRKSDAEQYLKNLYDLYTR.TTNLSSKLMEFNLGTDKQTFLSKLIKSIFISYLE.YIE
Retrocopy KLQGFVKDQLEECRKSDAEQYLKNLYDLYTR-TTNLSSKLMEFNLGTDKQTFLSKLIKSIFISYLEDYIE

Parental  VETGYLKSRSAMILQRYYDSKNHQKRSIGTGGIQDLKERIRQRTNLPLGPSIDTHGETFLSQEVVVNLLQ
          VETGYLKSRS.MILQRYYDSKNHQKRSIGTGGIQDLKERIRQRTNLPLGPSIDTHGETFLSQEVVVNLLQ
Retrocopy VETGYLKSRSGMILQRYYDSKNHQKRSIGTGGIQDLKERIRQRTNLPLGPSIDTHGETFLSQEVVVNLLQ

Parental  ETKQAFERCHRLSDPSDLPRNAFRIFTILVEFLCIEHIDYALETGLAGIPSSDSRNANLYFLDVVQQANT
          ETKQAFERCHRLSDPSDLPRNAFRIFTILVEFLCIEHIDYALETGLAGIPSSDSRNANLYFLDVVQQANT
Retrocopy ETKQAFERCHRLSDPSDLPRNAFRIFTILVEFLCIEHIDYALETGLAGIPSSDSRNANLYFLDVVQQANT

Parental  IFHLFDKQFNDHLMPLISSSPKLSECLQKKKEIIEQMEMKLDTGIDRTLNCMIGQMKHI-LAAEQKK-TD
          IFHLFDKQFNDHLMPLISSSPKLSECLQK.KEIIEQMEMKLDTGIDRTLNCMIGQMK.I...A...K.TD
Retrocopy IFHLFDKQFNDHLMPLISSSPKLSECLQKRKEIIEQMEMKLDTGIDRTLNCMIGQMKLI<ILAAEQKKTD

Parental  FKPEDENNVLIQYTNACVKVCAYVRKQVEKIKNSMDGKNVDTVLMELGVRFHRLIYEHLQQYSYSCMGGM
          FKPEDENNVLIQYTNACVKVCAYVRKQVEKIKNSMDGKNVDTVLMELGVRFHRLIYEHLQQYSYSCMGGM
Retrocopy FKPEDENNVLIQYTNACVKVCAYVRKQVEKIKNSMDGKNVDTVLMELGVRFHRLIYEHLQQYSYSCMGGM

Parental  LAICDVAEYRKCAKDFKIPMVLHLFDTLHALCNLLVVAPDNLKQVCSGEQLANLDKNILHSFVQLRADYR
          LAICDVAEYRKCAKDFKIPMVLHLFDTLHALCNLLVVAPDNLKQVCSGEQLANLDKNILHSFVQL.ADYR
Retrocopy LAICDVAEYRKCAKDFKIPMVLHLFDTLHALCNLLVVAPDNLKQVCSGEQLANLDKNILHSFVQLCADYR

Parental  SARLARHFS
          SARLARHFS
Retrocopy SARLARHFS

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	0.61 RPM	26.88 RPM
SRP017611_kidney	0.20 RPM	23.11 RPM
SRP017611_liver	0.46 RPM	6.63 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1593 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1593 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1593 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
Homo sapiens	ENSG00000070367	1 retrocopy	retro_hsap_2938,
Oryctolagus cuniculus	ENSOCUG00000000756	1 retrocopy	retro_ocun_1593 ,
Pongo abelii	ENSPPYG00000005848	1 retrocopy	retro_pabe_2517,
Pan troglodytes	ENSPTRG00000023297	1 retrocopy	retro_ptro_2057,