RetrogeneDB ID: retro_ocun_1102

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:77410153..77410882(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RABEFLA2
• Ensembl ID: ENSOCUG00000008481
• Aliases: EEF1A1, RABEFLA2
• Description: eukaryotic translation elongation factor 1 alpha 1 (EEF1A1), mRNA [Source:RefSeq mRNA;Acc:NM_001082339]

Sequence

>retro_ocun_1102
GGGAAAGGAAAAATTGGCATCCACACCATCATCACTGGACACGTAGATTCAGGCAGGTCCACCACTACTGACCGTCTAGT
CTACGAAGGTGGCAGAATCAAGAGAAGAACTGTTGAAAAGTTCAGGAAGGAGGCTGCCAGGATGGAAAAGGACTTCTGCA
AGTATTCCCAGGTCTTGGATAAACTGAAAGCTGAGTGTGAACTTGGTACCACCATCAACATCCCCCTGTGGAAATGTGAG
AGTGGCAAGTGTTACGTGACTGTCATTGATGTCCCTGGACACAGAGACTGCATCAGAAACACCAGTGCAGGCACGTCACA
GGCTGAACATGGGTCCTGGGTGTTGCTGCTGGTGTCGGGGAATGCGAAGCTGGTATCTCCAAGAATGGCAGAACCGTGAG
CACGCTCTTCTGGCTTATACACTGGGAGTGAAGCAACTAATTGTCGGTGTTAACAAAATGGGCTTCACTCACAGCCACTC
ACAGCCAGAAGAGATACAAGAAGTCAGTACCGACATCAAGAAAATTGGCTGCAACCCTGACACAGTACCATTTGTGCCAA
TTTCTGGTTAGAACCGTGATAACATGCTGGAGACAAGTGCTAATATGCGTTGGTTCAAGGGATGGAAAGTTTCCAGCAAA
GATGGCCATGTCATGGAACCACACTGCTGGAGGCCCTGGATTGCATTCCTCCACCAACCAGAGCGAATGGCAAGCCTCTG
CACTGCCCC

Alignment

ORF - retro_ocun_1102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.73 %
• Parental protein coverage: 53.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GKEKTHINIVVIGHVDSGKSTTTGHLIYKCGGIDKRTIEKFEKEAAEMGKGSFKYAWVLDKLKAERERGI
          GK.K..I.....GHVDSG.STTT..L.Y..G.I..RT.EKF.KEAA.M.K...KY..VLDKLKAE.E.G.
Retrocopy GKGKIGIHTIITGHVDSGRSTTTDRLVYEGGRIKRRTVEKFRKEAARMEKDFCKYSQVLDKLKAECELGT

Parental  TIDISLWKFETSKYYVTIIDAPGHRDFIKNMITGTSQADCA-VLIVAAGVGEFEAGISKNGQT-REHALL
          TI.I.LWK.E..K.YVT.ID.PGHRD.I.N...GTSQA....VL.VAAGVGE.EAGISKNG.T.REHALL
Retrocopy TINIPLWKCESGKCYVTVIDVPGHRDCIRNTSAGTSQAEHG<VLGVAAGVGECEAGISKNGRT<REHALL

Parental  AYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEPSANMP
          AYTLGVKQLIVGVNKM..T....S....EEI..EVST.IKKIG.NPDTV.FVPISG.N.DNMLE.SANM.
Retrocopy AYTLGVKQLIVGVNKMGFT---HSHSQPEEI-QEVSTDIKKIGCNPDTVPFVPISG*NRDNMLETSANMR

Parental  WFKGWKVTRKDGN-ASGTTLLEALDCILPPTRPTDKPLRLP
          WFKGWKV..KDG....GTTLLEALDCI.PPTR...KPL..P
Retrocopy WFKGWKVSSKDGH<CHGTTLLEALDCIPPPTRANGKPLHCP

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	1055.04 RPM
SRP017611_kidney	0.00 RPM	4707.70 RPM
SRP017611_liver	0.00 RPM	1113.73 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1102 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1102 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 149 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014534	3 retrocopies	retro_btau_114, retro_btau_115, retro_btau_192,
Canis familiaris	ENSCAFG00000013249	1 retrocopy	retro_cfam_1007,
Dipodomys ordii	ENSDORG00000009629	1 retrocopy	retro_dord_509,
Equus caballus	ENSECAG00000020363	2 retrocopies	retro_ecab_66, retro_ecab_93,
Equus caballus	ENSECAG00000022260	1 retrocopy	retro_ecab_802,
Erinaceus europaeus	ENSEEUG00000000342	3 retrocopies	retro_eeur_407, retro_eeur_492, retro_eeur_625,
Felis catus	ENSFCAG00000030977	14 retrocopies	retro_fcat_1021, retro_fcat_1388, retro_fcat_1569, retro_fcat_1683, retro_fcat_1825, retro_fcat_184, retro_fcat_1915, retro_fcat_220, retro_fcat_221, retro_fcat_334, retro_fcat_515, retro_fcat_566, retro_fcat_688, retro_fcat_737,
Homo sapiens	ENSG00000156508	27 retrocopies	retro_hsap_1093, retro_hsap_1181, retro_hsap_1567, retro_hsap_1671, retro_hsap_190, retro_hsap_2302, retro_hsap_2455, retro_hsap_2637, retro_hsap_2712, retro_hsap_278, retro_hsap_283, retro_hsap_2896, retro_hsap_2920, retro_hsap_2967, retro_hsap_2983, retro_hsap_3239, retro_hsap_3291, retro_hsap_3314, retro_hsap_363, retro_hsap_3701, retro_hsap_3706, retro_hsap_3758, retro_hsap_3825, retro_hsap_3917, retro_hsap_4220, retro_hsap_4730, retro_hsap_989,
Loxodonta africana	ENSLAFG00000028081	1 retrocopy	retro_lafr_651,
Myotis lucifugus	ENSMLUG00000013537	24 retrocopies	retro_mluc_110, retro_mluc_1252, retro_mluc_1392, retro_mluc_1430, retro_mluc_1558, retro_mluc_1628, retro_mluc_1644, retro_mluc_1853, retro_mluc_1901, retro_mluc_1910, retro_mluc_2071, retro_mluc_2148, retro_mluc_2154, retro_mluc_2277, retro_mluc_2355, retro_mluc_2358, retro_mluc_2359, retro_mluc_2391, retro_mluc_441, retro_mluc_470, retro_mluc_677, retro_mluc_950, retro_mluc_956, retro_mluc_966,
Monodelphis domestica	ENSMODG00000018533	4 retrocopies	retro_mdom_1053, retro_mdom_1146, retro_mdom_311, retro_mdom_792,
Mustela putorius furo	ENSMPUG00000003816	6 retrocopies	retro_mputfur_1514, retro_mputfur_1643, retro_mputfur_220, retro_mputfur_502, retro_mputfur_844, retro_mputfur_862,
Mustela putorius furo	ENSMPUG00000004271	10 retrocopies	retro_mputfur_1179, retro_mputfur_1276, retro_mputfur_1351, retro_mputfur_1394, retro_mputfur_284, retro_mputfur_355, retro_mputfur_474, retro_mputfur_678, retro_mputfur_920, retro_mputfur_973,
Mus musculus	ENSMUSG00000037742	15 retrocopies	retro_mmus_1349, retro_mmus_1518, retro_mmus_1667, retro_mmus_1783, retro_mmus_1816, retro_mmus_1849, retro_mmus_1850, retro_mmus_1864, retro_mmus_1909, retro_mmus_2363, retro_mmus_2583, retro_mmus_2902, retro_mmus_3249, retro_mmus_480, retro_mmus_483,
Oryctolagus cuniculus	ENSOCUG00000008481	3 retrocopies	retro_ocun_1102 , retro_ocun_187, retro_ocun_71,
Ochotona princeps	ENSOPRG00000016685	6 retrocopies	retro_opri_1049, retro_opri_1076, retro_opri_1197, retro_opri_298, retro_opri_325, retro_opri_383,
Sus scrofa	ENSSSCG00000004489	4 retrocopies	retro_sscr_169, retro_sscr_492, retro_sscr_612, retro_sscr_758,
Ictidomys tridecemlineatus	ENSSTOG00000007687	4 retrocopies	retro_itri_1509, retro_itri_1740, retro_itri_1816, retro_itri_195,
Tursiops truncatus	ENSTTRG00000000114	19 retrocopies	retro_ttru_1020, retro_ttru_1150, retro_ttru_1196, retro_ttru_1349, retro_ttru_1351, retro_ttru_1368, retro_ttru_1384, retro_ttru_1810, retro_ttru_1861, retro_ttru_1876, retro_ttru_384, retro_ttru_390, retro_ttru_401, retro_ttru_523, retro_ttru_664, retro_ttru_698, retro_ttru_844, retro_ttru_941, retro_ttru_998,
Drosophila melanogaster	FBgn0000557	1 retrocopy	retro_dmel_9,