RetrogeneDB ID: retro_ocun_1701

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018786:334665..335262(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EAPP
• Ensembl ID: ENSOCUG00000003226
• Aliases: None
• Description: E2F-associated phosphoprotein [Source:HGNC Symbol;Acc:19312]

Sequence

>retro_ocun_1701
TGCCTTACTGGGGAAAGTGAGTCATCTAGTGGAGATGATTTGAAAAAGAAATGGAAACTGAATTACATTCTACCATAAAA
ACAAGGGAGGACAGGTTATCTTCTCTGGGACAGGATCTGCCTCGGGAAATGGGAACGTTGGAATGGTTCTAACAAAGTAT
TATTATGACATCTCTTTTGATTCTGATCCTGAGGATGAAGACAAAGCAGCACAGGTGACGAGGAAGAAAAACAAGAAACG
ACACAGGATTCCAACAAATGATGAATTACTGTGTGATCCTGAAAAAGATAAGAGAGACCAGGCCTGGGCTGATGCACAGA
GAAGGGGTGATCGCGGGTTTGGACTCCAGAGACCAGGCCAACAGCAACAGCCGGTTGCAAATAGTGGTGCTGTTCTGAGT
TGCCCTGCCTGCATGACTGTGCTGTACCTTGATTGCCAGAGGCGTGACTCTTACAAAACTCAGTGCAGAGCAATGTTTGT
GATGAGCTGTTCTGTCAACAAAGAGGAGGTTCTAAAATACAAAGCCCCAGAGAACAGGAAGACCAAGCGGGGCGTGAGAG
GATGAGGTCTAACCATGCAGATGCTGGGAGAAGGCTG

Alignment

ORF - retro_ocun_1701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.85 %
• Parental protein coverage: 76.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CLTGESESSSEDE-FEKEMEAELNSTIQTMEDKLSSLG-TGSSSENGKVGTVLTKYYDDIYFDSDSEDED
          CLTGESESSS.D..FEKEME.EL.STI.T.ED.LSSLG.TGS.S.NG.VG.VLTKYY.DI.FDSD.EDED
Retrocopy CLTGESESSSGDD<FEKEMETELHSTIKTREDRLSSLG<TGSASGNGNVGMVLTKYYYDISFDSDPEDED

Parental  KAAQVTKKKKKKQHRIPTNDELLYDPEKDNRDQAWVDAQRRGYHGFGLQRPRQQQQPVPNSDAVLNCPAC
          KAAQVT.KK.KK.HRIPTNDELL.DPEKD.RDQAW.DAQRRG..GFGLQRP.QQQQPV.NS.AVL.CPAC
Retrocopy KAAQVTRKKNKKRHRIPTNDELLCDPEKDKRDQAWADAQRRGDRGFGLQRPGQQQQPVANSGAVLSCPAC

Parental  MTTLCLDCQRHESYKTQYRAMFVMNCSVNKEEVLRYKAPENRKKRR-GHKKMRSTHEDAAEQV
          MT.L.LDCQR..SYKTQ.RAMFVM.CSVNKEEVL.YKAPENRK..R.G...MRS.H.DA....
Retrocopy MTVLYLDCQRRDSYKTQCRAMFVMSCSVNKEEVLKYKAPENRKTKR<GRERMRSNHADAGRRL

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	26.77 RPM
SRP017611_kidney	0.00 RPM	34.66 RPM
SRP017611_liver	0.00 RPM	15.41 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1701 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1701 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1701 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005391	1 retrocopy	retro_cjac_3231,
Cavia porcellus	ENSCPOG00000003005	1 retrocopy	retro_cpor_898,
Myotis lucifugus	ENSMLUG00000013814	1 retrocopy	retro_mluc_596,
Monodelphis domestica	ENSMODG00000014525	1 retrocopy	retro_mdom_1226,
Mustela putorius furo	ENSMPUG00000001029	1 retrocopy	retro_mputfur_19,
Oryctolagus cuniculus	ENSOCUG00000003226	1 retrocopy	retro_ocun_1701 ,
Ictidomys tridecemlineatus	ENSSTOG00000005273	2 retrocopies	retro_itri_1598, retro_itri_237,
Tupaia belangeri	ENSTBEG00000001306	1 retrocopy	retro_tbel_4258,