RetrogeneDB ID: retro_ocun_1785

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018889:390514..391495(+)
• Located in intron of: ENSOCUG00000029691

Retrocopy information

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

Parental gene information

• Parental gene symbol: HAT1
• Ensembl ID: ENSOCUG00000005313
• Aliases: None
• Description: histone acetyltransferase 1 [Source:HGNC Symbol;Acc:4821]

Sequence

>retro_ocun_1785
CTTTTTGGGGATGATGAAAATGCTTTTGGTTACAAGGGACTGAAGATCTTATTATACTATATTGCTGGTAGCCTGTCAAC
AATGTTCGGTGTTGAATATGCATCTAAAGTAGAAGAGAACTTTGACTGTGTGGAGGCAGATGATGTTGAGGGCAGAATTA
GACAAATCATTCCACCTGGATTTAGCACAAACACGAATGATTTTCTTTCTTTGCTGGAAAAAGAAGTTGATTTCAAGCCA
TTTGGAACCTTACTCCATACATACTCAGTTCTCAGTCCCACAGGAGGAGAAAACTTCACATTTCAGATATATAAGACTGA
CATGACATGTACAGGCTTTCAAGAATATCATGAAAGGCTTCAGACCTTTTTGATGTGGTTTATTGAAACTGCTAGCTTTA
TTGACGTGGATGATGAAAGATAGCACTACTTTCTAGTATTTGAGAAGTATAATAAGGATGGAGCTACACTCTTTGCGACC
ATAGGCTACATGACAGTCTGTAATTACTATGTGTACCCAGACAAAACCTGGTCACATGTAAGTCAGATGCTGATATTGAC
TCCATTTCAAGGTCAAGGCCACGGTGCTCAACTTCTTGAAACAGTTCATAGATACTACATTGCGTCTCCTTCAGTTCTTG
ATATTACAGCAGAAGATCCATCCAAAAGCTATGTGAAATTAGGAGATTTTGTGCTTGTGAAACTTTGCCAAGATTTGCCC
TATTTTTCCTGAGAAAAGTTAATGCAAGGATTCAATGAAGAAATGGCAATAGAGGCACAACAAAAATTCAAAATAAATAA
GCAACATGCTAGACGGGTTTATGAAATTCTTCGACTCCTTGTAACTGACATGAGTAACGCTGAACAATATAGAAGATATA
GATTGGATATTAAAAGAAGACTAGCCCATATAAGAAAAAGAGAAAGATTTTGCTAAGATGAGAAAATGTCTCAGACCAGA
AGAACTGACAAACCAGATGAA

Alignment

ORF - retro_ocun_1785 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.54 %
• Parental protein coverage: 73.74 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LWCSSETAFGYKGLKILLYYIAGSLSTMFRVEYASKVDENFDCVEADDVEGKIRQIIPPGFCTNTNDFLS
          L....E.AFGYKGLKILLYYIAGSLSTMF.VEYASKV.ENFDCVEADDVEG.IRQIIPPGF.TNTNDFLS
Retrocopy LFGDDENAFGYKGLKILLYYIAGSLSTMFGVEYASKVEENFDCVEADDVEGRIRQIIPPGFSTNTNDFLS

Parental  LLEKEVDFKPFGTLLHTYSVLSPTGGENFTFQIYKADMTCTGFREYHERLQTFLMWFIETASFIDVDDER
          LLEKEVDFKPFGTLLHTYSVLSPTGGENFTFQIYK.DMTCTGF.EYHERLQTFLMWFIETASFIDVDDER
Retrocopy LLEKEVDFKPFGTLLHTYSVLSPTGGENFTFQIYKTDMTCTGFQEYHERLQTFLMWFIETASFIDVDDER

Parental  WHYFLVFEKYNKDGATLFATVGYMTVYNYYVYPDKTRPRVSQMLILTPFQGQGHGAQLLETVHRYYIASP
          .HYFLVFEKYNKDGATLFAT.GYMTV.NYYVYPDKT...VSQMLILTPFQGQGHGAQLLETVHRYYIASP
Retrocopy *HYFLVFEKYNKDGATLFATIGYMTVCNYYVYPDKTWSHVSQMLILTPFQGQGHGAQLLETVHRYYIASP

Parental  SVLDITAEDPSKSYVKLRDFVLVKLCQDLPCFSREKLMQGFNEEMAIEAQQKFKINKQHARRVYEILRLL
          SVLDITAEDPSKSYVKL.DFVLVKLCQDLP.FS.EKLMQGFNEEMAIEAQQKFKINKQHARRVYEILRLL
Retrocopy SVLDITAEDPSKSYVKLGDFVLVKLCQDLPYFS*EKLMQGFNEEMAIEAQQKFKINKQHARRVYEILRLL

Parental  VTDMSDAEQYRSYRLDIKRRLISPYKKKQ----RDLAKMRKCLRPEE
          VTDMS.AEQYR.YRLDIKRRL....K.............R....P.E
Retrocopy VTDMSNAEQYRRYRLDIKRRLAHIRKRERFC*DEKMSQTRRTDKPDE

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	17.83 RPM
SRP017611_kidney	0.10 RPM	22.30 RPM
SRP017611_liver	0.00 RPM	6.63 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1785 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1785 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1785 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011848	1 retrocopy	retro_dnov_2372,
Oryctolagus cuniculus	ENSOCUG00000005313	1 retrocopy	retro_ocun_1785 ,
Sorex araneus	ENSSARG00000005620	1 retrocopy	retro_sara_122,