RetrogeneDB ID: retro_ocun_207

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL019156:25708..26485(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023555
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000008783
• Aliases: None
• Description: None

Sequence

>retro_ocun_207
ATGAAAGAAGTAGATAACCTTGAAAGTATAAAAGAAGAATGGGTTTGCGAATCAGGATCTGACAATCAATGTCATAATAA
CAATCGACAAACGAATTGTGAGTATTTTGTTGACAGCCTTTTTGAGGAAGCACAGAAGGTTGGTGCCAAGTGCTTATCCC
CCACTGAACAAAAGAAACAGGTAGATGTAAGTATAAAGTTATGGAAAAACGGATTCACAGTCAATGATGATTTCAGAAGT
TATTCTGATGGTGCAAGTCAGCAGTTTCTGAACTCCATCAAAAAAGGGGAATTGCCTTCAGAATTACAGGGAGTTTTTGA
TAAAGAGGAGGTGGATGTGAAAGTTGAAGATAAGAAAAATGAAGTGTGCCTGTCAACAAAGCCTGTGTTCCAGCCATTTT
CAGGACAGGGCCACCGACTGGGAAGTGCCACACCAAAAATTGTTTCTAAAACAAAGATTCTTGAAGTTGAAAATAAAAGT
AATTTGTCTACTGTTCCACTGAACAACTTGGAACCCATCACTAATGTACGGATTTGGTTAGCCAATGGGAAAAGGATTGT
CCAGAAATTTAACATTTCTCATAGGGTAAGCCACATCAAAGACTTCATCGAGAAATACCAAGGATCTCAGAGAAGTCCAC
CTTTTTCCCTGGCAACAGCTCTTCCCTTCCTCAGATCACTCGATGAAACGCTTACACTGGAAGAAGCAGATCTGCAGAAT
GCTGTCATTATTCAAAGACTCCAAAAAACTGTGGAACCCTTTAGAGAACTTCCATAG

Alignment

ORF - retro_ocun_207 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.72 %
• Parental protein coverage: 99.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKKRNILAMSVSVVCESGSDNQCHNNNRQTNCEYFVDSLFEEAQKVGAKCLSPTEQKKQVDVSIKLWKNG
          K...N........VCESGSDNQCHNNNRQTNCEYFVDSLFEEAQKVGAKCLSPTEQKKQVDVSIKLWKNG
Retrocopy KEVDNLESIKEEWVCESGSDNQCHNNNRQTNCEYFVDSLFEEAQKVGAKCLSPTEQKKQVDVSIKLWKNG

Parental  FTVNDDFRSYSDGASQQFLNSIKKGELPSELQGVFDKEEVDVKVEDKKNEVCLSTKPVFQPFSGQGHRLG
          FTVNDDFRSYSDGASQQFLNSIKKGELPSELQGVFDKEEVDVKVEDKKNEVCLSTKPVFQPFSGQGHRLG
Retrocopy FTVNDDFRSYSDGASQQFLNSIKKGELPSELQGVFDKEEVDVKVEDKKNEVCLSTKPVFQPFSGQGHRLG

Parental  SATPKIVSKTKILEVENKSNLSTVPLNNLEPITNVRIWLANGKRIVQKFNISHRVSHIKDFIEKYQGSQR
          SATPKIVSKTKILEVENKSNLSTVPLNNLEPITNVRIWLANGKRIVQKFNISHRVSHIKDFIEKYQGSQR
Retrocopy SATPKIVSKTKILEVENKSNLSTVPLNNLEPITNVRIWLANGKRIVQKFNISHRVSHIKDFIEKYQGSQR

Parental  SPPFSLATALPFLRSLDETLTLEEADLQNAVIIQRLQKTVEPFRELP
          SPPFSLATALPFLRSLDETLTLEEADLQNAVIIQRLQKTVEPFRELP
Retrocopy SPPFSLATALPFLRSLDETLTLEEADLQNAVIIQRLQKTVEPFRELP

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	0.77 RPM	1.88 RPM
SRP017611_kidney	0.30 RPM	0.51 RPM
SRP017611_liver	0.23 RPM	0.46 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_207 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_207 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_207 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001640	5 retrocopies	retro_chof_1096, retro_chof_1171, retro_chof_2641, retro_chof_961, retro_chof_964,
Callithrix jacchus	ENSCJAG00000007665	1 retrocopy	retro_cjac_2085,
Equus caballus	ENSECAG00000020144	1 retrocopy	retro_ecab_569,
Echinops telfairi	ENSETEG00000002623	1 retrocopy	retro_etel_1116,
Homo sapiens	ENSG00000173960	1 retrocopy	retro_hsap_2025,
Gorilla gorilla	ENSGGOG00000002445	1 retrocopy	retro_ggor_1463,
Myotis lucifugus	ENSMLUG00000015640	1 retrocopy	retro_mluc_1195,
Macaca mulatta	ENSMMUG00000006487	1 retrocopy	retro_mmul_2068,
Mus musculus	ENSMUSG00000020634	1 retrocopy	retro_mmus_1007,
Nomascus leucogenys	ENSNLEG00000000751	1 retrocopy	retro_nleu_2612,
Oryctolagus cuniculus	ENSOCUG00000008783	1 retrocopy	retro_ocun_207 ,
Oryctolagus cuniculus	ENSOCUG00000023461	1 retrocopy	retro_ocun_563,
Otolemur garnettii	ENSOGAG00000000025	1 retrocopy	retro_ogar_1909,
Procavia capensis	ENSPCAG00000011502	4 retrocopies	retro_pcap_169, retro_pcap_255, retro_pcap_271, retro_pcap_323,
Pan troglodytes	ENSPTRG00000011705	1 retrocopy	retro_ptro_1347,
Rattus norvegicus	ENSRNOG00000004950	2 retrocopies	retro_rnor_1746, retro_rnor_2966,
Sorex araneus	ENSSARG00000010108	1 retrocopy	retro_sara_272,
Sus scrofa	ENSSSCG00000026283	1 retrocopy	retro_sscr_537,
Tupaia belangeri	ENSTBEG00000012158	1 retrocopy	retro_tbel_3887,