RetrogeneDB ID: retro_ocun_1413

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:50928317..50929308(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021966
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GAN
• Ensembl ID: ENSOCUG00000001073
• Aliases: None
• Description: gigaxonin [Source:HGNC Symbol;Acc:4137]

Sequence

>retro_ocun_1413
CAGATCAGGCTGAACGAAGACACAATCCAAGATGTCGTACAGGCTGCAGACCTGCTGCTGCTGACGGACCTTAAGACTCT
GTGCTGTGAGTTTTTAGAAGGCTGCATTGCTGCCGAGAACTGCATTGGGATCCGGGACTTTGCGCTGCATTACTGCCTGC
ACCACGTCCACTACCTGGCCACAGAATACCTGGAGACGCACTTCCGAGACGTCAGCAGCACTGAAGAATTCCTAGAACTG
AGCCCTCAGAAGCTCAGAGAAGTTACTTCTCTCGAGAAGTTGAACGTTGGCAATGAAAAATACGTATTTGAAGCCGTAAT
CCGGTGGCTAGCACATGACACAGAAATAAGAAAGGTCCACATGAAGGACGTGATGTCAGCGCTCTGGGTGTCGGGGCTGG
ACTCCAGCTACTTACGGGAACAGATGCTGAACGAACCACTAGTTCGAGAAATTGTCAAAGAGTGCAGCAACATCCCCCTC
AGCCAGCCGCAGCAAGGAGAGGCCGTGCTGGCCAACTTCAAGCCCCGGGGCTACTCGGAGTGCATCGTGACTGTCCGCGG
GGAGGAAAGAGTTTCCCGGAAACCAACGGCCGCGATGCGGTGCATGTGCCCTCTCTATGACCCCAACAGGCAGCTGTGGA
TCGAACTGGCGCCCTTGAGCATGCCGAGGATCAACCATGGCGTCCTCTCCGCAGAAGGATTTCTCTTTGTGTTTGGCGGC
CAAGATGAAAATAAGCAGACACTGAGCTCGGGAGAAAAGTTTGATCCGGATGCAAACACGTGGACTGCGCTGCCGCCCAT
GAATGCGGCAAGGCATAACTTTGGGATTGTGGAGATCGACCGAATGCTGTACATTTTAGGGGGGGAAGATGGTGAAAAAG
AGCTGATTTCCATGGAGTGTTAACGATATTTATTCTAAAACATGGACAAAGCAACTGGATTTGACCATGGTTAGAAAGAT
TGGCTGCTATGCACCTATGAAGAAGAAAATC

Alignment

ORF - retro_ocun_1413 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.37 %
• Parental protein coverage: 55.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QIRLNEDTIQDVVQAADLLLLTDLKTLCCEFLEGCIAAENCIGIRDFALHYCLHHVHYLATEYLETHFRD
          QIRLNEDTIQDVVQAADLLLLTDLKTLCCEFLEGCIAAENCIGIRDFALHYCLHHVHYLATEYLETHFRD
Retrocopy QIRLNEDTIQDVVQAADLLLLTDLKTLCCEFLEGCIAAENCIGIRDFALHYCLHHVHYLATEYLETHFRD

Parental  VSSTEEFLELSPQKLKEVISLEKLNVGNEKYVFEAVIRWIAHDTEIRKVHMKDVMSALWVSGLDSSYLRE
          VSSTEEFLELSPQKL.EV.SLEKLNVGNEKYVFEAVIRW.AHDTEIRKVHMKDVMSALWVSGLDSSYLRE
Retrocopy VSSTEEFLELSPQKLREVTSLEKLNVGNEKYVFEAVIRWLAHDTEIRKVHMKDVMSALWVSGLDSSYLRE

Parental  QMLNEPLVREIVKECSNIPLSQPQQGEAMLANFKPRGYSECIVTVGGEERVSRKPTAAMRCMCPLYDPNR
          QMLNEPLVREIVKECSNIPLSQPQQGEA.LANFKPRGYSECIVTV.GEERVSRKPTAAMRCMCPLYDPNR
Retrocopy QMLNEPLVREIVKECSNIPLSQPQQGEAVLANFKPRGYSECIVTVRGEERVSRKPTAAMRCMCPLYDPNR

Parental  QLWIELAPLSMPRINHGVLSAEGFLFVFGGQDENKQTLSSGEKYDPDANTWTALPPMNEARHNFGIVEID
          QLWIELAPLSMPRINHGVLSAEGFLFVFGGQDENKQTLSSGEK.DPDANTWTALPPMN.ARHNFGIVEID
Retrocopy QLWIELAPLSMPRINHGVLSAEGFLFVFGGQDENKQTLSSGEKFDPDANTWTALPPMNAARHNFGIVEID

Parental  GMLYILGGEDGEKELISMEC-YDIYSKTWTKQPDLTMVRKIGCYAAMKKKI
          .MLYILGGEDGEKELISMEC..DIYSKTWTKQ.DLTMVRKIGCYA.MKKKI
Retrocopy RMLYILGGEDGEKELISMEC>NDIYSKTWTKQLDLTMVRKIGCYAPMKKKI

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	0.06 RPM	5.41 RPM
SRP017611_kidney	0.00 RPM	5.78 RPM
SRP017611_liver	0.00 RPM	4.86 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1413 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1413 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1413 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000001073	1 retrocopy	retro_ocun_1413 ,