RetrogeneDB ID: retro_ocun_1648

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018740:1999427..2001317(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ILF3
• Ensembl ID: ENSOCUG00000013990
• Aliases: None
• Description: interleukin enhancer binding factor 3, 90kDa [Source:HGNC Symbol;Acc:6038]

Sequence

>retro_ocun_1648
GAGGCCGACAACGTGGACGTGCCGGCTGAGGACGAGAACAAAGAAGGGACTGGGGAGCAGAAGACGGAGCACATGACCAG
AACCCTGCGGGGCGTCATGCGGGTCGGCCTTGCAGCCAAGGGTCTCCTGCTCAAGGGGTCCTGGATCTGGAGCTGGTGCT
GCTCTGTAAGGAGAAGCCCACGGCTGCCCTCTTGGACAGGTGGCTGACAACCTGGCCATCCAGCTCACTGCCGTGACAGA
AGACAAATATGAGATCCTGCAGTCTGTGGACGATGCTACAATTGTGATAAAAAACACAAAAGAGCCTCCATTGTCCTTGA
CTATCCACCTGACCTCCCCCGTGGTCAGAGAAGAGATGGAGAAAGTATTAGCTGGAGAAACGCTATCAGTCAACGACCCC
CCGGACGTTCTGGACAAGCAGAAATGCCTTGCTGCCTTGGCGTCCCTCCGCCACGCCAAGTGGTTCCAGGCCAGAGCCAA
CGGGCTGAAGTTCTGTGTCATTGTCATCCGGGTCCTGAGGGACCTGTGCACCCGTGTGCCCACCTGGGGTCCTCTCAGAG
GATGGCCTCTGGAGCTCCTGTGCGAGAAGTCCATCGGCACAGCCAACAGACCCATGGGTGCCGGCGAGGCCCTGCGGAGG
GTGCTGGAGTGCCTGGCGTCAGGCATCGTGATGCCAGATGGTTCTGGCATTTATGACCCTTGTGAAAAAGAAGCCACTGA
TGCTATTGGGCATCTAGACAGACAGCAACGGGAAGATATCACACAGAGTGCGCAGCATGCACTGCGGCTTGCAGCATTTG
GCCAGCTCCATAAAGTCCTGGGCATGGACCCCCTGCCTTCCAAGATGCCCAAGTAACCAAAGAACGAAAACCCCGTGGAC
TACATCGTTCAAATCCCCCCCAGCACCACCTACGCCATCACCCCCATGAAGCGCCCAATGGAAGAGGATGGGGAGGAGAA
AGTCGCCCAGCAAAAAAGAAGATTCAGAAGAAAGAGGAGAAGGCTGAGCCGCCGCAGGCCATGAACGCGCTGATGCAGCT
GAACCAGCTGAAGCCGGGGCTGCAGTACAGGCTGGTCTCGCAGACCGGCCCCGTGCACGCGCCCATCTTCACCATGTCTG
TGGAGGTGGATGGCAATTCCTTCGAGGCCTCAGGGCCGTCCAAGAAGACTGCCAAGCTGCACGTGGCCGTCAAGGTGTTG
CAGGACATGGGCTTGCCCACGGGCACCGAGGGCAGGGACTCCAGCAAGGGGGAGGACTCGGCCGAGGAGACCGAGTCGAA
GCCTGCAGTGGTGGCCCCACCTCCTGTGGTGGAAGCCGTGTCCACCCCCAGCGCTGCCTTCCCCACGGATGCCACGGCTG
AGGGGCCGATCCTGACTAAGCATGGGAAGAACCCAGTCATGGAGCTGAACGAGAAGAGACGTGGCCTCAAGTAAAAGCTC
ATCTCCGAGACCGGGGGCAGCCACGACAAGCACTTTGTCATGGAGGTGGAGGTGGAGGGACAGAGGTTTCAAGGTGCTGG
CTCCAACAAAAAGGCGACAAAGGCCTACGCTGCCCTGGCAGCCCTGGAGAAGCTTTTCCCTGATGCCCCTCTCGCCCTGG
AAGCCAACAAGAAGAAAAGAGCCCCAGTCCCTGTCAGAGGCGGGCCGAAGTTTGCTGCCAAGCCGCATAACCCTGGCTTC
GGCATGGGAGGCCCCATGCACTATGAGGTGCCCCCGCCCCCCAACCTTCGAGGCCGGGGCAGAGGAGGGAACATCCGTGG
GTGAGGGCGAGGGCGAGGCAGAGGCTTTGGCGCCTACCACGGAGGCTACATGAACGCTGGCGCCGGGTACGACAGCTACG
GGTACGGAGGCAACTCGGCGACAGCAGGCTACAGTGACTTTTTCACAGAC

Alignment

ORF - retro_ocun_1648 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 70.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EADNVDVPAEDENKEGAGEQKTEHMTRTLRGVMRVGLVAKGLLLKGD-LDLELVLLCKEKPTAALLDK-V
          EADNVDVPAEDENKEG.GEQKTEHMTRTLRGVMRVGL.AKGLLLKG..LDLELVLLCKEKPTAALLD..V
Retrocopy EADNVDVPAEDENKEGTGEQKTEHMTRTLRGVMRVGLAAKGLLLKGS<LDLELVLLCKEKPTAALLDR<V

Parental  ADNLAIQLAAVTEDKYEILQSVDDAAIVIKNTKEPPLSLTIHLTSPVVREEMEKVLAGETLSVNDPPDVL
          ADNLAIQL.AVTEDKYEILQSVDDA.IVIKNTKEPPLSLTIHLTSPVVREEMEKVLAGETLSVNDPPDVL
Retrocopy ADNLAIQLTAVTEDKYEILQSVDDATIVIKNTKEPPLSLTIHLTSPVVREEMEKVLAGETLSVNDPPDVL

Parental  DRQKCLAALASLRHAKWFQARANGLKSCVIVIRVLRDLCTRVPTWGPLRGWPLELLCEKSIGTANRPMGA
          D.QKCLAALASLRHAKWFQARANGLK.CVIVIRVLRDLCTRVPTWGPLRGWPLELLCEKSIGTANRPMGA
Retrocopy DKQKCLAALASLRHAKWFQARANGLKFCVIVIRVLRDLCTRVPTWGPLRGWPLELLCEKSIGTANRPMGA

Parental  GEALRRVLECLASGIVMPDGSGIYDPCEKEATDAIGHLDRQQREDITQSAQHALRLAAFGQLHKVLGMDP
          GEALRRVLECLASGIVMPDGSGIYDPCEKEATDAIGHLDRQQREDITQSAQHALRLAAFGQLHKVLGMDP
Retrocopy GEALRRVLECLASGIVMPDGSGIYDPCEKEATDAIGHLDRQQREDITQSAQHALRLAAFGQLHKVLGMDP

Parental  LPSKLPKKPKNENPVDYTVQIPPSTTYAITPMKRPMEEDGEEKSPSKKK-KKIQKKEEKAEPPQAMNALM
          LPSK.PK.PKNENPVDY.VQIPPSTTYAITPMKRPM.E...E......K.KKIQKKEEKAEPPQAMNALM
Retrocopy LPSKMPK*PKNENPVDYIVQIPPSTTYAITPMKRPM-EEDGEEKVAQQK<KKIQKKEEKAEPPQAMNALM

Parental  RLNQLKPGLQYKLVSQTGPVHAPIFTMSVEVDGNSFEASGPSKKTAKLHVAVKVLQDMGLPTGTEGRDSS
          .LNQLKPGLQY.LVSQTGPVHAPIFTMSVEVDGNSFEASGPSKKTAKLHVAVKVLQDMGLPTGTEGRDSS
Retrocopy QLNQLKPGLQYRLVSQTGPVHAPIFTMSVEVDGNSFEASGPSKKTAKLHVAVKVLQDMGLPTGTEGRDSS

Parental  KGEDSAEETESKPAVVAPPPVVEAVSTPSAAFPTDATAENVKQQGPILTKHGKNPVMELNEKRRGLKYEL
          KGEDSAEETESKPAVVA.PP.V..........P..A........GPILTKHGKNPVMELNEKRRGLK..L
Retrocopy KGEDSAEETESKPAVVA-PPPV----VEAVSTPSAAFPTDATAEGPILTKHGKNPVMELNEKRRGLK*KL

Parental  ISETGGSHDKRFVMEVEVDGQKFQGAGSNKKVAKAYAALAALEKLFPDAPLALEANKKKRAPVPVRGGPK
          ISETGGSHDK.FVMEVEV.GQ.FQGAGSNKK..KAYAALAALEKLFPDAPLALEANKKKRAPVPVRGGPK
Retrocopy ISETGGSHDKHFVMEVEVEGQRFQGAGSNKKATKAYAALAALEKLFPDAPLALEANKKKRAPVPVRGGPK

Parental  FAAKPHNPGFGMGGPMHNEVPPPPNLRGRGRGGNIR--GRGRGRGFGANHGGYMNAGAGYGSYGYGGNSA
          FAAKPHNPGFGMGGPMH.EVPPPPNLRGRGRGGNIR..GRGRGRGFGA.HGGYMNAGAGY.SYGYGGNSA
Retrocopy FAAKPHNPGFGMGGPMHYEVPPPPNLRGRGRGGNIRG*GRGRGRGFGAYHGGYMNAGAGYDSYGYGGNSA

Parental  TAGYSQFYSN
          TAGYS.F...
Retrocopy TAGYSDFFTD

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	0.50 RPM	170.42 RPM
SRP017611_kidney	0.51 RPM	136.02 RPM
SRP017611_liver	0.15 RPM	66.28 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1648 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1648 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1648 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000008365	1 retrocopy	retro_mluc_2581,
Oryctolagus cuniculus	ENSOCUG00000005430	1 retrocopy	retro_ocun_1216,
Oryctolagus cuniculus	ENSOCUG00000013990	1 retrocopy	retro_ocun_1648 ,
Oryctolagus cuniculus	ENSOCUG00000016737	1 retrocopy	retro_ocun_1813,