RetrogeneDB ID: retro_ocun_67

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:113650520..113651306(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000011333
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000027895
• Aliases: None
• Description: None

Sequence

>retro_ocun_67
GAAAATGCGGAGGGAGAGCAGCTTGAGGCATCATTAAATGCACTGCTGAGCCAAGTGGCAGAGCTGAAGAACTCCCTGGG
AAGCTTCATTTACAAGCTGGAGCATGATAGGCTAAGCTGGCCCTCTGTCCAGGACAGTTTTGCCTTGCTCTCTGGGTGGT
TGAACACTCTGAACAAGGTTGTGAAGCGTGAAAAGACACCACTGCCCTGCACCCAGGTCACCATCCCTCTGGTGTTATCC
CCAGACCGAGAGCATGATCTCATGAGGCAGACTGAAGGACGGGTGCTTATCTTCAGCCATCAGGTGGTCCCTGACCATCT
AAGAACCAAGCCTGACCCTGAGGTTGAAGAGAAAGAGAAGCAACTTAAGACACATGCTGCCTGCATTGGTGCTGATGCAG
CTCAGAAGCAGATCCAGAGCTTGAATACAATGTGCTCAAACCTTCTGGAGAAAATCAGCAAAGAGGAGCAAGAATCAGAG
AGTGGAGGTCTCTGGCCAAACAAGCGGACATTTAACCCCGCAGACACCAATGCCCTGGTGGCAGCTGTTGCCTTTGGGAA
GGGGCTGTCCAATTGGAGACCTTCAGGCAGCAGTGGTCCTGGCCAGCCAGGTCAGCCAGGAGCTGGGGCCATCCTTGCAG
GAGCCTTGGGACTACAACAGGTGCAGATGGCAGGAGCTCCAGGCCAGCAGCAGCCAATGCTTAATGGAGTGCAAATGGCT
CAAGCAGGTCAACCAGGGAAAAAGCCAAGTGGAATAAAAACCAATATCAAGTCAGCTTCAATGTAA

Alignment

ORF - retro_ocun_67 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.69 %
• Parental protein coverage: 95.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEKQLEASLDALLSQVADLKNSLGSFIYKLENEYDRLTWPSVLDSFALLSGQLNTLNKVLKHEKTPLFRN
          E..QLEASL.ALLSQVA.LKNSLGSFIYKLE...DRL.WPSV.DSFALLSG.LNTLNKV.K.EKTPL...
Retrocopy EGEQLEASLNALLSQVAELKNSLGSFIYKLE--HDRLSWPSVQDSFALLSGWLNTLNKVVKREKTPLPCT

Parental  QVIIPLVLSPDRDEDLMRQTEGRVPVFSHEVVPDHLRTKPDPEVEEQEKQLTTDAARIGADAAQKQIQSL
          QV.IPLVLSPDR..DLMRQTEGRV..FSH.VVPDHLRTKPDPEVEE.EKQL.T.AA.IGADAAQKQIQSL
Retrocopy QVTIPLVLSPDREHDLMRQTEGRVLIFSHQVVPDHLRTKPDPEVEEKEKQLKTHAACIGADAAQKQIQSL

Parental  NKMCSNLLEKISKEERESESGGLRPNKQTFNPADTNALVAAVAFGKGLSNWRPSGSSGPGQPGQPGAGAI
          N.MCSNLLEKISKEE.ESESGGL.PNK.TFNPADTNALVAAVAFGKGLSNWRPSGSSGPGQPGQPGAGAI
Retrocopy NTMCSNLLEKISKEEQESESGGLWPNKRTFNPADTNALVAAVAFGKGLSNWRPSGSSGPGQPGQPGAGAI

Parental  LAGASGLQQVQMAGAPGQQQPMLSGVQMAQAGQPGKMPSGIKTNIKSASM
          LAGA.GLQQVQMAGAPGQQQPML.GVQMAQAGQPGK.PSGIKTNIKSASM
Retrocopy LAGALGLQQVQMAGAPGQQQPMLNGVQMAQAGQPGKKPSGIKTNIKSASM

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	13.96 RPM
SRP017611_kidney	0.00 RPM	10.74 RPM
SRP017611_liver	0.00 RPM	9.09 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_67 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_67 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_67 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005237	1 retrocopy	retro_cfam_458,
Erinaceus europaeus	ENSEEUG00000002286	1 retrocopy	retro_eeur_117,
Macropus eugenii	ENSMEUG00000013567	1 retrocopy	retro_meug_1813,
Myotis lucifugus	ENSMLUG00000012621	1 retrocopy	retro_mluc_1618,
Monodelphis domestica	ENSMODG00000011310	1 retrocopy	retro_mdom_1131,
Oryctolagus cuniculus	ENSOCUG00000027895	2 retrocopies	retro_ocun_1088, retro_ocun_67 ,
Otolemur garnettii	ENSOGAG00000001865	1 retrocopy	retro_ogar_2091,
Ictidomys tridecemlineatus	ENSSTOG00000009737	1 retrocopy	retro_itri_818,