RetrogeneDB ID: retro_ocun_91

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:55945157..55945967(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000000726
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000004413
• Aliases: None
• Description: None

Sequence

>retro_ocun_91
ATGGGGAACTGCTGCTGGACACAGTGCTTCGGGCTGCTCCGCAAAGAAGCGGGGCGGCTGCAGCGTGTAGGAGGCGGCGG
AGGATCCAAGTATTTTAGAACATGCTCAGGAGGTGAGCACTTAACTATAGAGTTTGAGAATCTAGTAGAAAGTGATGAAG
GGGAAAGTCCAGAAAGCAGTCATAGACCTCTTACTGAGGAAGAAATTGTTGACCTAAGAGAAAGACATTATGATTCTATT
GCTGAAAAACAGAAAGACATTGATAAGAAAATTCAAAAAGAGCAAGAAAGGCAGAGAGTTGCACAGCGATGTCATCCTTC
CAACAATGGAGAATATCGAAGTTCAGGACCAGAAGATGACTTTGAATCTTGTTTGAGAAATATAAAGTCACAGTATGAAG
TTTTTCGAAGTAGTAGACTCTCGTCTGATGCCACATTTCTTACACCAAATACAGAAAGCAGTTGTGATTTAATGACCAAA
ACTAAATCAACTAGTGGAAATGATGACAGCACATCCTTAGACCTAGAGTGGGAAGATGAAGAAGGGATGACTAGAATGCT
TCCCATGAGAGAATGTTCCAAAACAGAGGAAGACATTCTCCGGGCAGCACTGAAGTGCAGCAGCAAGAAGACTGGAAGTA
ATCCGACATCAGCCTCTGATGATTCCAATGGGCTGGAGTGGGAGAATGATTTTGTTAGTGCGGAAATGGATGATAATGGC
AATTCTGAGTATTCTGGGTTTGTAAATCCTGTATTAGAACTGTCTGATTCTGCCATGCAGCAGTATGATACAGATCAGCA
GACTCGATAG

Alignment

ORF - retro_ocun_91 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.89 %
• Parental protein coverage: 68.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LQEEKLRLEEEALYAAQREAARAAKQRKLLEQERQRVAQRCHPSNNGEYQSSGPEDDFESCLRNIKSQYE
          L.EE......E..Y....E...........EQERQRVAQRCHPSNNGEY.SSGPEDDFESCLRNIKSQYE
Retrocopy LTEEEIVDLRERHYDSIAEKQKDIDKKIQKEQERQRVAQRCHPSNNGEYRSSGPEDDFESCLRNIKSQYE

Parental  VFRSSRLSSDATVLTPNTESSCDLMTKTKSTSGNDDSTSLDLEWEDEEGMTRMLPMRERSKTEEDILRAA
          VFRSSRLSSDAT.LTPNTESSCDLMTKTKSTSGNDDSTSLDLEWEDEEGMTRMLPMRE.SKTEEDILRAA
Retrocopy VFRSSRLSSDATFLTPNTESSCDLMTKTKSTSGNDDSTSLDLEWEDEEGMTRMLPMRECSKTEEDILRAA

Parental  LKCSSKKTGSNPTSASDDSNGLEWENDFVSAEMDDNGNSEYSGFVNPVLELSDSAMQQYDTDQQTR
          LKCSSKKTGSNPTSASDDSNGLEWENDFVSAEMDDNGNSEYSGFVNPVLELSDSAMQQYDTDQQTR
Retrocopy LKCSSKKTGSNPTSASDDSNGLEWENDFVSAEMDDNGNSEYSGFVNPVLELSDSAMQQYDTDQQTR

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	2.10 RPM	20.92 RPM
SRP017611_kidney	0.10 RPM	12.67 RPM
SRP017611_liver	0.00 RPM	6.32 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_91 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_91 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_91 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007262	2 retrocopies	retro_chof_1995, retro_chof_8,
Monodelphis domestica	ENSMODG00000005746	1 retrocopy	retro_mdom_160,
Oryctolagus cuniculus	ENSOCUG00000004413	1 retrocopy	retro_ocun_91 ,
Otolemur garnettii	ENSOGAG00000001631	1 retrocopy	retro_ogar_1054,
Sus scrofa	ENSSSCG00000009128	1 retrocopy	retro_sscr_245,