RetrogeneDB ID: retro_ocun_541

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:142766214..142767345(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PARL
• Ensembl ID: ENSOCUG00000007882
• Aliases: None
• Description: presenilin associated, rhomboid-like [Source:HGNC Symbol;Acc:18253]

Sequence

>retro_ocun_541
ATGGCGTGGCAAGGCTGGGCACAGAGAAGCTGGGGCTGCAGCCAGGCGTGGGCTTTAGGGGGCTGCAGCCCCGAGGAACT
CACTACGGCCTTGGCCCCACTGTGGCTGCTCGGATGCAGGTTTAATTTCTTTATTCAGCAAAAATCTGGACTCAGAAAAG
CACTGAGGAAGGTTGAACCTGGAAGATCAGACACAGGGACAAGTGGCGAAACATACAAGAGAAGTGCTTTGATTCCTCCT
GTGGAAGAAACAGCATTTTACCCATCTCCGTATCCTATAAGGACTCTTGTGAAACCGTTGTTTCTTGCTGTTGGGTTTAC
AGGCTGTGCATTTGGATCAGCTGCTATTTGGCAGTATGAATCACTGAAATCCAGGGTCCAGAGTTATTTTGATGGTATAA
AAGCTGATTGGTTGGATAGCATAAGGCCACAAAAAGAAGGAGACTTCAGAAAGGAGATTAACAAATGGCAGAATAACCTA
AGTGATGGCCAGCGGACTGTGACAGGTATCATAGCTGCAAATGTATTTGTATTCTGTTTATGGAGAGTACCTTCTCTACA
GCAGACAATGATTAAATATTTCACATCTAATCCAGCCTCAAAGGTCCTTTGTTCTCCAATGTTGCTGTCAACATGCAGTC
ATTTCTCCTTATTTCACACGGCAGCAAATATGTATGTTTTATGAAGCTTCTCCTCCAGCATAGTGAACATCCTGGGTCAA
GAACAATTCATGGCAGTGTACCTGTCTGCAGGTGTTATTTCCAATTTTGTCAGTTATGTATGTAAAGGTGCCACAGGAAG
ACATGGACCATCACTTGGTACATCCGGTGCCATCATGACCGTCCTTGCTGCTGTCTGCACCAAGATCCCTGATGGGAAGC
TCGCCATCATCTTCCTCCCCATGTTCACCTTAGCAGCCAGCAATGCCCTAAAAGCCATTATTGCCATGGATACAGCGGGA
AGGATCCTAGGATGGAAATTTTTTGATCATGCAGCACATCTTGGGGGAGCTCTCTTTGGAATATGGTACATTACTTACGG
TCATGAACTCATTTGGAAGAACAGGGAGCCTCTGGTGAAAATCTGGCACGAAATGAGGACTGATGGCCCCAGAAAAGGCG
GTGGCTCTAAG

Alignment

ORF - retro_ocun_541 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAWRGWAQRSWGCGQAWALGGRSPEELTTALAPPRLLGRRFNFFIQQKSGFRKAPRKVEPRRSDTGTSGE
          MAW.GWAQRSWGC.QAWALGG.SPEELTTALAP..LLG.RFNFFIQQKSG.RKA.RKVEP.RSDTGTSGE
Retrocopy MAWQGWAQRSWGCSQAWALGGCSPEELTTALAPLWLLGCRFNFFIQQKSGLRKALRKVEPGRSDTGTSGE

Parental  TYKRSALIPPVEETVFYPSPYPIRTLVKPLFFTVGFTGCAFGSAAIWQYESLKSRVQSYFDGIKADWLDS
          TYKRSALIPPVEET.FYPSPYPIRTLVKPLF..VGFTGCAFGSAAIWQYESLKSRVQSYFDGIKADWLDS
Retrocopy TYKRSALIPPVEETAFYPSPYPIRTLVKPLFLAVGFTGCAFGSAAIWQYESLKSRVQSYFDGIKADWLDS

Parental  IRPQKEGDFRKEINKWWNNLSDGQRTVTGIIAANVFVFCLWRVPSLQRTMIKYFTSNPASKVLCSPMLLS
          IRPQKEGDFRKEINKW.NNLSDGQRTVTGIIAANVFVFCLWRVPSLQ.TMIKYFTSNPASKVLCSPMLLS
Retrocopy IRPQKEGDFRKEINKWQNNLSDGQRTVTGIIAANVFVFCLWRVPSLQQTMIKYFTSNPASKVLCSPMLLS

Parental  TFSHFSLFHMAANMYVLWSFSSSIVNILGQEQFMAVYLSAGVISNFVSYVCKVATGRYGPSLGASGAIMT
          T.SHFSLFH.AANMYVL.SFSSSIVNILGQEQFMAVYLSAGVISNFVSYVCK.ATGR.GPSLG.SGAIMT
Retrocopy TCSHFSLFHTAANMYVL*SFSSSIVNILGQEQFMAVYLSAGVISNFVSYVCKGATGRHGPSLGTSGAIMT

Parental  VLAAVCTKIPDGKLAIIFLPMFTFTAGNALKAIIAMDTAGMILGWKFFDHAAHLGGALFGIWYITYGHEL
          VLAAVCTKIPDGKLAIIFLPMFT..A.NALKAIIAMDTAG.ILGWKFFDHAAHLGGALFGIWYITYGHEL
Retrocopy VLAAVCTKIPDGKLAIIFLPMFTLAASNALKAIIAMDTAGRILGWKFFDHAAHLGGALFGIWYITYGHEL

Parental  IWKNREPLVKIWHEMRTNGPRKGGGSK
          IWKNREPLVKIWHEMRT.GPRKGGGSK
Retrocopy IWKNREPLVKIWHEMRTDGPRKGGGSK

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	0.06 RPM	21.47 RPM
SRP017611_kidney	0.20 RPM	31.22 RPM
SRP017611_liver	0.08 RPM	11.18 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_541 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_541 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_541 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000014935	1 retrocopy	retro_dord_315,
Myotis lucifugus	ENSMLUG00000004507	1 retrocopy	retro_mluc_883,
Mus musculus	ENSMUSG00000033918	2 retrocopies	retro_mmus_1882, retro_mmus_3526,
Oryctolagus cuniculus	ENSOCUG00000007882	1 retrocopy	retro_ocun_541 ,
Pongo abelii	ENSPPYG00000014338	2 retrocopies	retro_pabe_2290, retro_pabe_2912,
Ictidomys tridecemlineatus	ENSSTOG00000023222	1 retrocopy	retro_itri_380,