RetrogeneDB ID: retro_ocun_1386

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:154807521..154808417(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIAT1
• Ensembl ID: ENSOCUG00000007819
• Aliases: None
• Description: hippocampus abundant transcript 1 [Source:HGNC Symbol;Acc:23363]

Sequence

>retro_ocun_1386
ATGCCCCAGGGGAAGAAGAAGAAATGGGCCGGGAGCCGCAGGATCATGCTGGCCAAGAAGATCATCATCAGGGACGGAGG
CACGCCTCCAGGGATAGGTTCTCCTGGTGTTTATATGCAGTTATTGTGATCTTTTGGAGTTTCTTGCTTTGGGACTGCTG
ACAGCACCTACCCTGGTGGTATTACATGAAACTTTCCCTAAACATACATTCCTGATGAATGGCCCAATTCAAGGAGTAAA
AGGTTTGTTGTCATTCCTCAGTGCCCCACTTATTGGCGCTCTTTCTGATGTTTGGGGCCCAAAATCGTTCCTGCTGCTAA
CAGTATTTCTCACATGTGCCCCAATTCCCTTAATGAAGATCAGCCCATGGTGGTGCTTTGCTGTTATCTCTGTTTCTGGG
GTGCCTGCAGTGACTTTCTCCGTGGTATTTGCTTATGTAGCAGATATAACCCAAGAGCATGAAAGAAGTATGGCTTATGG
ATGGTTTCAGCAACATTTGCTGCAAGTTTAGTCACCAACCCTGCAATTGGAGCTCACCTTAGACGACTATATGGGGACAG
TTTAGTGGTGGCGTTAGCTACAACAGTAGCTCTGTTAGGTTATCTGTTTCATCCTTGTTGCTGTATCCAGAGTCATTGTC
TGAGAAGATGTGGCCAGCATTGTGGGGTGCGACCATTACCTGGGAGCAGGCTGATCCCTTTGCATCCTTAAAAAAATTGG
GCCAGGATTCCATAGTGCTGCTAATCTGCATTACCAGGTTTCTCTCCTACCTACCAGAGGCAGGCCAATATTCCAGCTTT
TTGTTATACCTCAGACAGATAATGAAATTTTCACCAAAAAGCACTGCAGCATTTATAGCAGTCCTTGGCATTCTTTCCAT
TATTGCACAAACCCTA

Alignment

ORF - retro_ocun_1386 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.51 %
• Parental protein coverage: 60.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MTQGKKKKRAANRSIMLAKKIIIKDGGTPQGIGSPSVY-HAVIVIF-LEFFAWGLLTAPTLVVLHETFPK
          M.QGKKKK.A..R.IMLAKKIII.DGGTP.GIGSP.VY..AVIVIF.LEF.A.GLLTAPTLVVLHETFPK
Retrocopy MPQGKKKKWAGSRRIMLAKKIIIRDGGTPPGIGSPGVY<YAVIVIF<LEFLALGLLTAPTLVVLHETFPK

Parental  HTFLMNGLIQGVKGLLSFLSAPLIGALSDVWGRKSFLLLTVFFTCAPIPLMKISPWWYFAVISVSGVFAV
          HTFLMNG.IQGVKGLLSFLSAPLIGALSDVWG.KSFLLLTVF.TCAPIPLMKISPWW.FAVISVSGV.AV
Retrocopy HTFLMNGPIQGVKGLLSFLSAPLIGALSDVWGPKSFLLLTVFLTCAPIPLMKISPWWCFAVISVSGVPAV

Parental  TFSVVFAYVADITQEHERSMAYG-LVSATFAASLVTSPAIGAYLGRVYGDSLVVVLATAIALLD-ICFIL
          TFSVVFAYVADITQEHERSMAYG..VSATFAASLVT.PAIGA.L.R.YGDSLVV.LAT..ALL..ICFIL
Retrocopy TFSVVFAYVADITQEHERSMAYG<MVSATFAASLVTNPAIGAHLRRLYGDSLVVALATTVALLG>ICFIL

Parental  VAV-PESLPEKMRPASWGAPISWEQADPFASLKKVGQDSIVLLICITVFLSYLPEAGQYSSFFLYLRQIM
          VAV.PESL.EKM.PA.WGA.I.WEQADPFASLKK.GQDSIVLLICIT.FLSYLPEAGQYSSF.LYLRQIM
Retrocopy VAV>PESLSEKMWPALWGATITWEQADPFASLKKLGQDSIVLLICITRFLSYLPEAGQYSSFLLYLRQIM

Parental  KFSPESVAAFIAVLGILSIIAQTI
          KFSP.S.AAFIAVLGILSIIAQT.
Retrocopy KFSPKSTAAFIAVLGILSIIAQTL

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	42.50 RPM
SRP017611_kidney	0.00 RPM	46.02 RPM
SRP017611_liver	0.00 RPM	15.88 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1386 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1386 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1386 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010468	1 retrocopy	retro_chof_2174,
Echinops telfairi	ENSETEG00000005809	1 retrocopy	retro_etel_2047,
Myotis lucifugus	ENSMLUG00000002112	1 retrocopy	retro_mluc_718,
Oryctolagus cuniculus	ENSOCUG00000007819	1 retrocopy	retro_ocun_1386 ,
Drosophila melanogaster	FBgn0035400	1 retrocopy	retro_dmel_13,