RetrogeneDB ID: retro_ocun_532

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:122997750..122998372(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIN28B
• Ensembl ID: ENSOCUG00000017850
• Aliases: None
• Description: lin-28 homolog B (C. elegans) [Source:HGNC Symbol;Acc:32207]

Sequence

>retro_ocun_532
ATGAGATTTGGACTCATCTCCATGATAAACCGAGAGGGAAGCCCCTTGAATATTCTAGTCGATGTGTTTGTACACCAAAG
TAAACTATTCATGGAAGGATTTAGAAGCCTAAAAGGAGAACCAGTGGAATTCACATTTAAAAAAAATCTTCCAAAGGCCT
TGAATCAATAAGGGTAACAGGACCTGGTGGGAGCTCCTGTTTAGAAAGTAAAAGAAGACTCAAAGAGAAGACAGGGCAGA
AAAGAAAACCAAAGGGAGATAGATGCTACAACTGCCGTGGCCTTGATCATCATGCAAAGAAATGCAGTCTACCTCCTCAG
CCAAAGACGTGCCATTGCTGTCAGAGCCTCCTGCACATGGTGGCAAACTGCCCACATTCAGCTGTTGCACAGCCACCTGC
CAGTTCTCAGGGAAGACGGGAAGCAGCGTCCCAGCCATGCACTTGGATGTTTCCTAGAAAAAGTGGAAGGAGGGCAGGGC
TGCATGTCACCACCGTTAGCTCATGAGGCAAGGCCAGAGGTCCTAGAGTTCCAGGCAGGTCCCCTCTAGAAGCTTCCTCC
ATGAAGTCGTCACAGAAGAACCAAACAAAAAGGGGCCTTCAGTTCAAAAAAGGAAAAAGACA

Alignment

ORF - retro_ocun_532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.07 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGFGFISMINREGSPLDIPVDVFVHQSKLFMEGFRSLKEGEPVEFTFKKS-SKGL-ESIRVTGPGGSPCL
          M.FG.ISMINREGSPL.I.VDVFVHQSKLFMEGFRSLK.GEPVEFTFKK...K.L.ESIRVTGPGGS.CL
Retrocopy MRFGLISMINREGSPLNILVDVFVHQSKLFMEGFRSLK-GEPVEFTFKKNLPKAL<ESIRVTGPGGSSCL

Parental  GSERRPKGKTLQKRKPKGDRCYNCGGLDHHAKECSLPPQPKKCHCCQSILHMVANCPHKTAAQPPASSQG
          .S.RR.K.KT.QKRKPKGDRCYNC.GLDHHAK.CSLPPQPK.CHCCQS.LHMVANCPH...AQPPASSQG
Retrocopy ESKRRLKEKTGQKRKPKGDRCYNCRGLDHHAKKCSLPPQPKTCHCCQSLLHMVANCPHSAVAQPPASSQG

Parental  RQEAESQPCTSMFPREAG-GGQGCTSPPFAQEARPEVLE-RPGRSPPEASSTKSSAAPEEPNKKG-PSVQ
          R.EA.SQPCT.MFPR..G.GGQGC.SPP.A.EARPEVLE..PGRSP.EASS.KSS.......K.G.PSVQ
Retrocopy RREAASQPCTWMFPRKSG>GGQGCMSPPLAHEARPEVLE<VPGRSPLEASSMKSS--QKNQTKRG<PSVQ

Parental  KRKKT
          KRKKT
Retrocopy KRKKT

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	0.11 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_532 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_532 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_532 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000015340	1 retrocopy	retro_etel_1927,
Microcebus murinus	ENSMICG00000002297	4 retrocopies	retro_mmur_1377, retro_mmur_1390, retro_mmur_660, retro_mmur_800,
Oryctolagus cuniculus	ENSOCUG00000000299	1 retrocopy	retro_ocun_19,
Oryctolagus cuniculus	ENSOCUG00000017850	1 retrocopy	retro_ocun_532 ,
Otolemur garnettii	ENSOGAG00000011042	1 retrocopy	retro_ogar_645,
Sorex araneus	ENSSARG00000008374	2 retrocopies	retro_sara_121, retro_sara_746,
Tarsius syrichta	ENSTSYG00000006480	1 retrocopy	retro_tsyr_1815,