RetrogeneDB ID: retro_ocun_1878

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:29001252..29001922(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALKBH3
• Ensembl ID: ENSOCUG00000016359
• Aliases: None
• Description: alkB, alkylation repair homolog 3 (E. coli) [Source:HGNC Symbol;Acc:30141]

Sequence

>retro_ocun_1878
ACCTGGTCAGACCTGGAGAAGGAGCATCATCTGAAAGAGTCTGTGTTCAAAGAATCAAACAAGTAGTACATAGCCTTCCA
GAGCCACAAATGATTAATAGGGAGGGAGGTCATAAAATCAGCCTGTTACCCACAAGTCTATCTAGGGAGCATTTGTACCC
TGGCATTGTTGATTTAAAAGAAGCCAACTGGGCATTTAAACAAGTTTGTCAGGATGTTCCCTGGAAACAGAAGACAGCAT
CAAAGAGGATATAATTTATCAACAACCAAGACTTGTAGCATGGGCATGGAGAACTTCCTTATACCTATTCAAGAATCCCT
ATGCAACCAAATTCTCATTATCAGCCTGTGCTGAGCACATTGAAGAACCACATCAAAGAGAACACCAGATACATGTTTAA
CAACTTACCCTGCAATCTTTACTGAAATAACAACAGTGGAGACTGGTATAGCAATGAGTAACCCTTATCAGGGAGGTGCC
CCATCATTGCCTTGCTCAATTTGGATGCCATATGTACTTCTGAGATGAGGAAGAAGCCCCCACCAGAAGAGAGCAGAAAC
CACACATATGAGGAGAGAGTTAAGATACCTCTGATCACAGGACTGCATTAATCACAGAGGGATCTGTACAAGCTAACTGG
CAGCATCGAGGGCCCAAAGAAAACCACTCT

Alignment

ORF - retro_ocun_1878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.74 %
• Parental protein coverage: 78.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TWRSKEHPLPDREFVFREP-QQVVRPVPEPRVIDREGVYEISLSPTGVSTSRVRLYPGFIDLKEADWMLE
          TW...E......E.VF.E...QVV...PEP..I.REG...ISL.PT..S.SR..LYPG..DLKEA.W...
Retrocopy TWSDLEKEHHLKESVFKES<KQVVHSLPEPQMINREGGHKISLLPT--SLSREHLYPGIVDLKEANWAFK

Parental  RLCQDVPWKQRTG-IRENITYQQPRLTAW-YGELPYTYSRITMEPNPHWHPVLSTLKRRIEENTGYSFNS
          ..CQDVPWKQ.T..I.E.I.YQQPRL.AW..GELPYTYSRI.M.PN.H..PVLSTLK..I.ENT.Y.FN.
Retrocopy QVCQDVPWKQKTA<IKEDIIYQQPRLVAW>HGELPYTYSRIPMQPNSHYQPVLSTLKNHIKENTRYMFNN

Parental  LLCNLYRNEKDSVDWHSDDEPSLGRCPVIASLSFGATRTFEMRKKPSVEENGDYTYVERVKIPL-DHGTL
          L.CNLY.N...S.DW.S...P..GRCP.IA.L...A..T.EMRKKP..EE....TY.ERVKIPL.DH.T.
Retrocopy LPCNLY*N-NNSGDWYSNE*PLSGRCPIIALLNLDAICTSEMRKKPPPEESRNHTYEERVKIPL<DHRTA

Parental  LIMEGATQADWQHRVPKEYHS
          LI.EG..QA.WQHR.PKE.HS
Retrocopy LITEGSVQANWQHRGPKENHS

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	6.46 RPM
SRP017611_kidney	0.00 RPM	5.07 RPM
SRP017611_liver	0.00 RPM	4.93 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1878 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1878 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000019863	1 retrocopy	retro_mdom_1850,
Oryctolagus cuniculus	ENSOCUG00000016359	1 retrocopy	retro_ocun_1878 ,