RetrogeneDB ID: retro_ocun_4

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:107990374..107991028(+)
• Located in intron of: ENSOCUG00000005736

Retrocopy information

• Ensembl ID: ENSOCUG00000006620
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000004065
• Aliases: None
• Description: None

Sequence

>retro_ocun_4
ATGAGCAGCAAAGTCTCTCGCGACACCCTGTACGAGGCGGTGCAGGAAGTCCTGCACGGGAACCAGCGCAAGCGCCAGAA
GTTTCTGGAGACGGTGGAGCTGCAGATCAGCTTGAAGAATTATGACCCCCAGAAAGACAAACGCTTCTCGGGCACCGTCA
GGCTGAAGTCCACCCCCCGCCCCAAGTTCTCCGTGTGTGTCCTGGGCGACCAGCAGCACTGCGACGAGGCCAAGGCTGTG
GACATCCCCCACATGGACATCGAGGCGCTCAAGAAGCTCAACAAGAACAAGAAGCTAGTCAAGAAGCTGGTCAAGAAGTA
TGACGCCTTTTTGGCCTCAGAGTCTCTGATTAAGCAGATCCCACGAATCCTGGGCCCAGGCCTAAATAAGGCTGGCAAGT
TCCCCTCCCTGCTGACACACAATGAGAACATGGTGGCCAAAGTCGATGAGGTGAAGTCCACAATCAAGTTCCAGATGAAG
AAGGTGCTGTGTCTGGCTGTGGCAGTTGGCCACGTGAAGATGACAGACGATGAGCTTGTGTACAACATCCACCTGGCTGT
CAACTTCCTGGTGTCACTGCTGAAGAAGAATTGGCAGAATGTCCGGGCTTTGTACATCAAGAGCACCATGGGCAAGCCCC
AGCGCCTGTACTAA

Alignment

ORF - retro_ocun_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.62 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGD
          MSSKVSRDTLYEAV.EVLHGNQRKR.KFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGD
Retrocopy MSSKVSRDTLYEAVQEVLHGNQRKRQKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRPKFSVCVLGD

Parental  QQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTH
          QQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKL.KKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTH
Retrocopy QQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLVKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLTH

Parental  NENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTM
          NENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTM
Retrocopy NENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKSTM

Parental  GKPQRLY
          GKPQRLY
Retrocopy GKPQRLY

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	0.94 RPM	97.90 RPM
SRP017611_kidney	1.42 RPM	180.92 RPM
SRP017611_liver	0.31 RPM	67.75 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_4 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_4 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_4 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 139 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000670	13 retrocopies	retro_amel_1144, retro_amel_1223, retro_amel_1262, retro_amel_1591, retro_amel_1813, retro_amel_198, retro_amel_318, retro_amel_320, retro_amel_417, retro_amel_520, retro_amel_609, retro_amel_710, retro_amel_970,
Canis familiaris	ENSCAFG00000001318	18 retrocopies	retro_cfam_1118, retro_cfam_1200, retro_cfam_1222, retro_cfam_124, retro_cfam_1501, retro_cfam_1775, retro_cfam_1867, retro_cfam_2002, retro_cfam_2141, retro_cfam_281, retro_cfam_337, retro_cfam_347, retro_cfam_413, retro_cfam_847, retro_cfam_907, retro_cfam_911, retro_cfam_920, retro_cfam_986,
Echinops telfairi	ENSETEG00000013325	2 retrocopies	retro_etel_1974, retro_etel_326,
Felis catus	ENSFCAG00000012904	7 retrocopies	retro_fcat_1144, retro_fcat_1488, retro_fcat_1561, retro_fcat_1971, retro_fcat_210, retro_fcat_262, retro_fcat_560,
Homo sapiens	ENSG00000198755	13 retrocopies	retro_hsap_142, retro_hsap_1462, retro_hsap_1710, retro_hsap_177, retro_hsap_1935, retro_hsap_2795, retro_hsap_3025, retro_hsap_3245, retro_hsap_3353, retro_hsap_337, retro_hsap_3949, retro_hsap_4025, retro_hsap_4040,
Gorilla gorilla	ENSGGOG00000028140	10 retrocopies	retro_ggor_1, retro_ggor_1124, retro_ggor_1282, retro_ggor_1407, retro_ggor_2088, retro_ggor_2273, retro_ggor_234, retro_ggor_2702, retro_ggor_358, retro_ggor_57,
Macropus eugenii	ENSMEUG00000005760	6 retrocopies	retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Myotis lucifugus	ENSMLUG00000000080	10 retrocopies	retro_mluc_1053, retro_mluc_1526, retro_mluc_1611, retro_mluc_1815, retro_mluc_1963, retro_mluc_1964, retro_mluc_2519, retro_mluc_751, retro_mluc_902, retro_mluc_918,
Macaca mulatta	ENSMMUG00000015907	6 retrocopies	retro_mmul_1931, retro_mmul_2041, retro_mmul_2321, retro_mmul_2330, retro_mmul_306, retro_mmul_583,
Monodelphis domestica	ENSMODG00000013766	2 retrocopies	retro_mdom_276, retro_mdom_499,
Nomascus leucogenys	ENSNLEG00000008650	13 retrocopies	retro_nleu_1174, retro_nleu_1210, retro_nleu_1697, retro_nleu_1778, retro_nleu_1980, retro_nleu_2055, retro_nleu_2342, retro_nleu_2436, retro_nleu_2879, retro_nleu_662, retro_nleu_838, retro_nleu_986, retro_nleu_989,
Ornithorhynchus anatinus	ENSOANG00000014574	1 retrocopy	retro_oana_86,
Oryctolagus cuniculus	ENSOCUG00000004065	2 retrocopies	retro_ocun_130, retro_ocun_4 ,
Pan troglodytes	ENSPTRG00000018085	13 retrocopies	retro_ptro_1157, retro_ptro_1293, retro_ptro_142, retro_ptro_167, retro_ptro_1892, retro_ptro_2041, retro_ptro_2134, retro_ptro_2193, retro_ptro_2681, retro_ptro_269, retro_ptro_2729, retro_ptro_2737, retro_ptro_994,
Pteropus vampyrus	ENSPVAG00000002763	9 retrocopies	retro_pvam_1107, retro_pvam_1223, retro_pvam_123, retro_pvam_1294, retro_pvam_1440, retro_pvam_345, retro_pvam_722, retro_pvam_775, retro_pvam_906,
Rattus norvegicus	ENSRNOG00000000505	4 retrocopies	retro_rnor_2302, retro_rnor_37, retro_rnor_400, retro_rnor_43,
Sarcophilus harrisii	ENSSHAG00000002047	1 retrocopy	retro_shar_438,
Ictidomys tridecemlineatus	ENSSTOG00000023366	3 retrocopies	retro_itri_1097, retro_itri_524, retro_itri_847,
Tursiops truncatus	ENSTTRG00000009431	6 retrocopies	retro_ttru_100, retro_ttru_1137, retro_ttru_1325, retro_ttru_1477, retro_ttru_205, retro_ttru_494,