RetrogeneDB ID: retro_ocun_222

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 9:29695733..29696375(+)
• Located in intron of: ENSOCUG00000002826

Retrocopy information

• Ensembl ID: ENSOCUG00000027457
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000010549
• Aliases: None
• Description: None

Sequence

>retro_ocun_222
ATGCGATTCAAGAATCGATTCCAGCGGTTCATGAACCATCGAGCCCCCGCCAATGGCCGCTACAAACCGACTTGCTATGA
ACACGCTGCTAACTGTTACACACATGCATTCCTCATTGTTCCGGCCATCGTGGGCAGTGCCCTCCTCCATCGACTGTCTG
ACGACTGCTGGGAAAAGATAACAGCATGGATTTATGGCATGGGCCTCTGTACCCTCTTCATTGTTTCCACAGTATTTCAC
ATCGTCTCATGGAAAAAGAGCCACTTGAGGTTAAATCTCCGTGAACTTGGACCCCTGGCATCTCATATGCGTTGGTTTAT
CTGGCTCATGGCAGCTGGAGGAACAATTTATGTGTTTCTCTACCATGAAAAGTATAATGTGGTTGAGCCTTTTTTCTATC
TCACAATGGGATTCTCCCCGGCCTTGGTGGTGACATCAATGACTAACACCGACGGACTGCATGAACTTGCCTGTCGGGGC
TTAATTTATTGCTTGGGAGTTGTGTTCTTCAAGAGCGATGGCATCATTCCATTTGTCCATGCCATCTGGCACCTGTTTGT
GGCCACAGCAGCTGCGGTGCATTACTATGCCATTTGGAAGTACCTTTACCGAAGTCCTACGGACTTTGTGCGACACTTAT
GA

Alignment

ORF - retro_ocun_222 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.93 %
• Parental protein coverage: 51.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LNLRELGPLASHMRWFIWLMAAGGTIYVFLYHEKYKVVELFFYLTMGFSPALVVTSMTNTDGLHELACGG
          LNLRELGPLASHMRWFIWLMAAGGTIYVFLYHEKY.VVE.FFYLTMGFSPALVVTSMTNTDGLHELAC.G
Retrocopy LNLRELGPLASHMRWFIWLMAAGGTIYVFLYHEKYNVVEPFFYLTMGFSPALVVTSMTNTDGLHELACRG

Parental  LIYCLGVVFFKSDGIIPFAHAIWHLFVATAAAVHYYAIWKYLYRSPTDFMRHL
          LIYCLGVVFFKSDGIIPF.HAIWHLFVATAAAVHYYAIWKYLYRSPTDF.RHL
Retrocopy LIYCLGVVFFKSDGIIPFVHAIWHLFVATAAAVHYYAIWKYLYRSPTDFVRHL

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	1.77 RPM	118.05 RPM
SRP017611_kidney	0.51 RPM	13.78 RPM
SRP017611_liver	0.00 RPM	0.62 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_222 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_222 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000205	1 retrocopy	retro_btau_777,
Choloepus hoffmanni	ENSCHOG00000013437	1 retrocopy	retro_chof_1814,
Dasypus novemcinctus	ENSDNOG00000017248	1 retrocopy	retro_dnov_2313,
Macropus eugenii	ENSMEUG00000007054	1 retrocopy	retro_meug_714,
Myotis lucifugus	ENSMLUG00000012876	1 retrocopy	retro_mluc_289,
Monodelphis domestica	ENSMODG00000014847	5 retrocopies	retro_mdom_1029, retro_mdom_1569, retro_mdom_1591, retro_mdom_670, retro_mdom_951,
Oryctolagus cuniculus	ENSOCUG00000010549	1 retrocopy	retro_ocun_222 ,
Otolemur garnettii	ENSOGAG00000005902	2 retrocopies	retro_ogar_3070, retro_ogar_3071,
Procavia capensis	ENSPCAG00000004969	1 retrocopy	retro_pcap_231,
Ictidomys tridecemlineatus	ENSSTOG00000016227	1 retrocopy	retro_itri_913,
Tursiops truncatus	ENSTTRG00000007915	1 retrocopy	retro_ttru_469,