RetrogeneDB ID: retro_ocun_1879

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:30098958..30099684(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000008407
• Aliases: None
• Description: None

Sequence

>retro_ocun_1879
AGGGAAAAAAGGCAGGTTCCTGATGTGCCAGAAATGCTTAACAAAAAGGGGGGGAATTTCACAGAGCTCAAGATCAAGAG
CCCAAGAAAGAAGTTTACCCAAAATATGCTTCAAAGGCAAGAAGGAAGCTGATCTATGAAAAAGCTGAGCATTATCACAA
GGCATATAGGCACACGTACGGAACTGAAATTCAAATGGCGAGGAAGGCGAGAAAAGCTGGCAACATCTATGCACCTGCAG
AGCCCAAACTGGCATTTGTCATCAGGATCCGCAGTATCCATGGTGTAAGCTCCAAAGTCCTAAGCGTGTTGCAGTCTCTT
CACCTTTGCCATCTCTTCAACAGCACTTTTGTTGAGTTCAATAAGACTTCGACTCACATGCCAAGGACTGTGGGAACATG
TATTGCCTGGAGGTACCTGAATCTGAAAGCAGTAAATGAACTAATGTACAAGGATGGTTATGGCAAAATCAGTAAGAAGT
GAGTTGCCTTGACAGACAACGCTCTTATTGCCCAATCTCTTAGTAAATATGTTATCATGTGCATGGAGGATCTGATTCAT
GAGATCCATACTGTTGGAAGACACATCAGAGATCCAGTAACTTCCTGGGGCCCTTCAAGTTCTTTTCCACACAGGGGATG
AAGGAAGAAGACCACCTATTTTGTAGAGGGTGAAGATAGGGGCAATAGGGGAAGACCAGATCAGCAGGCTGATTAGAAGG
ATGAGT

Alignment

ORF - retro_ocun_1879 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.42 %
• Parental protein coverage: 97.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  REKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLR-KARRKLIYEKAKHYHKEYRQMYRTEIRMARM
          REK..VP.VPE.L.KK..NF.ELKIK..RKKF.Q.ML..KARRKLIYEKA.HYHK.YR..Y.TEI.MAR.
Retrocopy REKRQVPDVPEMLNKKGGNFTELKIKSPRKKFTQNMLQ<KARRKLIYEKAEHYHKAYRHTYGTEIQMARK

Parental  ARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASINMLRIVEPYIAWGY
          ARKAGN.Y.PAEPKLAFVIRIR.I.GVS.KV..VLQ.L.L...FN.TFV..NK.S..M.R.V...IAW.Y
Retrocopy ARKAGNIYAPAEPKLAFVIRIRSIHGVSSKVLSVLQSLHLCHLFNSTFVEFNKTSTHMPRTVGTCIAWRY

Parental  PNLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGKYNIICMEDLIHEIYTVGKHFKE-ANNFLWPFKL
          .NLK.VNEL.YK.GYGKI.KK..ALTDN.LIA.SL.KY.I.CMEDLIHEI.TVG.H......NFL.PFK.
Retrocopy LNLKAVNELMYKDGYGKISKK*VALTDNALIAQSLSKYVIMCMEDLIHEIHTVGRHIRD<SSNFLGPFKF

Parental  SSPRGGMK-KKTTHFVEGGDAGNR-EDQINRLIRRMN
          .S...GMK.KKTT.FVEG.D.GNR.EDQI.RLIRRM.
Retrocopy FSTQ-GMK>KKTTYFVEGEDRGNR>EDQISRLIRRMS

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	179.03 RPM
SRP017611_kidney	0.00 RPM	399.55 RPM
SRP017611_liver	0.00 RPM	123.63 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1879 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1879 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1879 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017654	15 retrocopies	retro_dnov_1561, retro_dnov_1692, retro_dnov_182, retro_dnov_1893, retro_dnov_209, retro_dnov_2158, retro_dnov_2568, retro_dnov_264, retro_dnov_2657, retro_dnov_279, retro_dnov_287, retro_dnov_365, retro_dnov_655, retro_dnov_77, retro_dnov_971,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Loxodonta africana	ENSLAFG00000017110	10 retrocopies	retro_lafr_140, retro_lafr_169, retro_lafr_334, retro_lafr_462, retro_lafr_47, retro_lafr_524, retro_lafr_694, retro_lafr_707, retro_lafr_816, retro_lafr_909,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Oryctolagus cuniculus	ENSOCUG00000003844	6 retrocopies	retro_ocun_1393, retro_ocun_1604, retro_ocun_1818, retro_ocun_278, retro_ocun_509, retro_ocun_598,
Oryctolagus cuniculus	ENSOCUG00000008407	12 retrocopies	retro_ocun_109, retro_ocun_1164, retro_ocun_1282, retro_ocun_1342, retro_ocun_1494, retro_ocun_1646, retro_ocun_1879 , retro_ocun_456, retro_ocun_501, retro_ocun_718, retro_ocun_727, retro_ocun_785,
Pteropus vampyrus	ENSPVAG00000009292	10 retrocopies	retro_pvam_105, retro_pvam_109, retro_pvam_1192, retro_pvam_1221, retro_pvam_151, retro_pvam_287, retro_pvam_308, retro_pvam_68, retro_pvam_69, retro_pvam_995,
Sus scrofa	ENSSSCG00000006182	3 retrocopies	retro_sscr_1138, retro_sscr_209, retro_sscr_796,