RetrogeneDB ID: retro_ocun_1254

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 4:38670300..38671040(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DYNC1LI2
• Ensembl ID: ENSOCUG00000006143
• Aliases: None
• Description: dynein, cytoplasmic 1, light intermediate chain 2 [Source:HGNC Symbol;Acc:2966]

Sequence

>retro_ocun_1254
CGTGAGCCCATGGATAAAATGAAAATTCCGCCAGAAGGAATGAGGGAGCGGAACGGAAGTTTGGGAAATATTTCCAAGGC
TATATCAAGTTTGAGGAAGGTTGTCAAGATTCCCCACAGCTGAAAGGGCCTCTGCCCACAGGCTCGGGTGAGGAGCATGC
TGCCTTGCCCCTGGTGAAAACGTGCGAACTCACAACATGGGGGCCCTGCGTTGGCAGTGTGCGCAAAGTGGGATGCAGTG
AGCATCCCAAAGAAGGGGCAGGACTACAGCCAGCAGCACCTGGACTTCATCCAGTCTCACCTGTGCAGGTTCTGCCTCCA
GGATGGGGCTGCCTTGATGCACACAATCAGTGAAGAAAGAGGAAAACCTCAACTTGTTGCATAAGTACCTTGTGCATAAA
ACATGTGGGTTCCATTTTACCACACCTGCCTTAGCTGTGGAAAAGGGTGCAGTTTTTATACCTGCAGGCTGGGATGGTAA
AAAGAATATAGCTATTATTACATGAAAACTTCACAACCGTGAAGCCCAAAGATGCATATGAAGACTTTGTCCTGAAACCT
GCTGTGAGAAAGCTGGTCCACGACAAAGGGTTGGCAGTAGAGGGTATGCAGGTGTTCCTAAGGAAGCAATAATCACCCCT
TGCGTAGCAGCCAGCCATGCCCACGCCAGCGTCGCAATCCTCTGCAGGAGGACCTGCTGGCTCTCCAAGTACCCAGGGCC
CGGGCGGGCCAGCCAGTATG

Alignment

ORF - retro_ocun_1254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.24 %
• Parental protein coverage: 50.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  REHIDKMKIPPEEMRE-LERKFVKDFQDYIEPEEGCQGSPQRRGPLTAGSDEESVALPL-GDNVLTHNLG
          RE..DKMKIPPE.MRE..ERKF.K.FQ.YI..EEGCQ.SPQ..GPL..GS.EE..ALPL.G.NV.THN.G
Retrocopy REPMDKMKIPPEGMRE<AERKFGKYFQGYIKFEEGCQDSPQLKGPLPTGSGEEHAALPL<GENVRTHNMG

Parental  I-PVLVVCTKCDAVSVLEKEHDYRDEHLDFIQSHLRRFCLQYGAALIYT-SVKEEKNLDLLYKYIVHKTY
          ..P.L.VC.K.DAVS...K..DY...HLDFIQSHL.RFCLQ.GAAL..T.SVK.E.NL.LL.KY.VHKT.
Retrocopy A<PALAVCAKWDAVSIPKKGQDYSQQHLDFIQSHLCRFCLQDGAALMHT>SVKKEENLNLLHKYLVHKTC

Parental  GFHFTTPALVVEKDAVFIPAGWDNEKKIAI-LHENFTTVKPEDAYEDFIVKPPVRKLVHDKELAAEDEQV
          GFHFTTPAL.VEK.AVFIPAGWD..K.IAI.LHENFTTVKP.DAYEDF..KP.VRKLVHDK.LA.E..QV
Retrocopy GFHFTTPALAVEKGAVFIPAGWDGKKNIAI>LHENFTTVKPKDAYEDFVLKPAVRKLVHDKGLAVEGMQV

Parental  FLMKQQSLLAKQPVTPTRASESPARGPSGSPRTQGRGGPASV
          FL.KQ.S.LA.QP..PT.AS.S.A.GP.GSP.TQG.GGPAS.
Retrocopy FLRKQ*SPLA*QPAMPTPASQSSAGGPAGSPSTQGPGGPASM

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	151.88 RPM
SRP017611_kidney	0.00 RPM	53.31 RPM
SRP017611_liver	0.00 RPM	23.43 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1254 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1254 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1254 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000006143	1 retrocopy	retro_ocun_1254 ,