RetrogeneDB ID: retro_ocun_426

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 10:38210043..38210975(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KPNA2
• Ensembl ID: ENSOCUG00000015913
• Aliases: None
• Description: karyopherin alpha 2 (RAG cohort 1, importin alpha 1) [Source:HGNC Symbol;Acc:6395]

Sequence

>retro_ocun_426
ATATCATCTTTGGCATGCAGTTACTTATGTAATCTTACACGGACACTTTCAAACCTTTGTGTCAACAAGAATCCTGCACC
CCTATTAGATGCCATTGAGCAGATTCTTCCTACTTTAGTTCATCTCCTGCATCACGATGATCCGGAAGTGTTAGCAGATA
CCTGCTGGGCAATTTCCTATCTCACATTTGTCCAAATGAACAAATTGCAATGGTTGTGAAGACAGGAGGTGTGCCCCAAC
TCGTGACGTTTCTAGGAGTTAATGAATTGCCAATTGTGACTCCTGCACTAAGGTGCCATAGGGAATATTGTCACAGGGAC
AGATGAACAGACTTAGGTTGTGATAGATGCAGGAGCACTTGCGATCTTTCCCAGCCTGCTGACTACCTCAAAACTAACAT
TCAGAAGGAGGCTACATGGACAATGTCAAACATCACAACTGGACGTCAGGACCAGATACAGCAAGTTGTGAATCACAGAT
TGGTCCCATTCTTTGTTGGTGTTCTCTCTAAGGCAGACTTTAAGACACAAAAAGAAGAAGTATGGGCTGTAACCAACTAT
ACAAGTGGTGGAACAGATGAACAGACTGTATACTTTGTTCATTGTGGTATAATAGAACCATTGATGAACCTCTTGACTGC
AAAAGATACCAAAATTATTCTGGTTATTCTGGATGTCATTTCAAATATCTTCCAGGCTGCTGAGAAATTAAGTGAAACTG
AGAAACTTAGTATAATGATTGAAGAATGTGGAGGCTTGAACAAAATTGAAGCTCTTCAAAACTGTGAAAATGAATCTGTG
AATAGGGCTTCATTAAACTTGATTGAGAAGTACTTCTCTATAGAGGAAGAGAAAGATCAAAATGTTGTGCCAGAAACCAT
CTCTGAAGGTTACACCTTCCAAGTACAGGATGGGGCAGGGGCTTTTAACTTT

Alignment

ORF - retro_ocun_426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 58.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSSLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTDGPNERIE
          .SSLAC.YL.NLT.TLSNLC.NKNPAP.LDA.EQILPTLV.LLHHDDPEVLADTCWAISYLT........
Retrocopy ISSLACSYLCNLTRTLSNLCVNKNPAPLLDAIEQILPTLVHLLHHDDPEVLADTCWAISYLTFVQMNKLQ

Parental  -MVVKTGVVPQLVKLLGANDLPIVTPALR-AIGNIVTGTDEQTQVVIDAGALAVFPSLLTNP-KTNIQKE
          .MVVKTG.VPQLV..LG.N.LPIVTPALR.AIGNIVTGTDEQT.VVIDAGALA.FPSLLT...KTNIQKE
Retrocopy <MVVKTGGVPQLVTFLGVNELPIVTPALR>AIGNIVTGTDEQT*VVIDAGALAIFPSLLTTS<KTNIQKE

Parental  ATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAVWAVTNYTSGGTVEQIVYLVHCGIIEP
          ATWTMSNIT.GRQDQIQQVVNH.LVPF.VGVLSKADFKTQKE.VWAVTNYTSGGT.EQ.VY.VHCGIIEP
Retrocopy ATWTMSNITTGRQDQIQQVVNHRLVPFFVGVLSKADFKTQKEEVWAVTNYTSGGTDEQTVYFVHCGIIEP

Parental  LMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYRASLNLIEK
          LMNLLTAKDTKIILVILD.ISNIFQAAEKL.ETEKLSIMIEECGGL.KIEALQN.ENESV.RASLNLIEK
Retrocopy LMNLLTAKDTKIILVILDVISNIFQAAEKLSETEKLSIMIEECGGLNKIEALQNCENESVNRASLNLIEK

Parental  YFSIEEEEDQNVAPETTSEGYTFQVQDGAPGAFHF
          YFSIEEE.DQNV.PET.SEGYTFQVQDGA.GAF.F
Retrocopy YFSIEEEKDQNVVPETISEGYTFQVQDGA-GAFNF

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	9.22 RPM
SRP017611_kidney	0.10 RPM	11.05 RPM
SRP017611_liver	0.00 RPM	6.40 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_426 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_426 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_426 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018411	3 retrocopies	retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus	ENSBTAG00000012225	1 retrocopy	retro_btau_1830,
Canis familiaris	ENSCAFG00000011598	2 retrocopies	retro_cfam_648, retro_cfam_90,
Cavia porcellus	ENSCPOG00000026318	1 retrocopy	retro_cpor_46,
Dasypus novemcinctus	ENSDNOG00000019151	6 retrocopies	retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus	ENSECAG00000020573	2 retrocopies	retro_ecab_1017, retro_ecab_1123,
Echinops telfairi	ENSETEG00000004445	2 retrocopies	retro_etel_346, retro_etel_347,
Felis catus	ENSFCAG00000001936	2 retrocopies	retro_fcat_1176, retro_fcat_921,
Myotis lucifugus	ENSMLUG00000027946	7 retrocopies	retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta	ENSMMUG00000018256	3 retrocopies	retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica	ENSMODG00000003897	1 retrocopy	retro_mdom_271,
Mus musculus	ENSMUSG00000018362	1 retrocopy	retro_mmus_229,
Oryctolagus cuniculus	ENSOCUG00000015913	4 retrocopies	retro_ocun_1765, retro_ocun_1916, retro_ocun_426 , retro_ocun_690,
Otolemur garnettii	ENSOGAG00000027672	7 retrocopies	retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii	ENSPPYG00000008569	1 retrocopy	retro_pabe_3501,
Rattus norvegicus	ENSRNOG00000015329	1 retrocopy	retro_rnor_42,
Sarcophilus harrisii	ENSSHAG00000011391	1 retrocopy	retro_shar_165,