RetrogeneDB ID: retro_ocun_1581

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018702:7266359..7267160(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPA2
• Ensembl ID: ENSOCUG00000010746
• Aliases: None
• Description: non imprinted in Prader-Willi/Angelman syndrome 2 [Source:HGNC Symbol;Acc:17044]

Sequence

>retro_ocun_1581
AAAAAAAAAGGATTTCTGCGACTTGCCGAAAAAGGTTCCATGAGAGCACATTAAGGTGGCTGTGCATATCTGAAAGAATG
GTTGTGGTGGGCTGGACTGCAGTCAAGGGGAGTTGGGGAGGTGGCCAACTTTGCTGCTTATGCATTTGCACCAGCTCCGA
TAGGAGCTCTCAGCGTACTCATAAGTGCCATTCTTTCTTCATACTTTCTAAATGAAAGACCTCATCTTCATGGGAAAATT
GAATATTTGCTAAGCATTCTGGCATCTACAGTTATGTCATTCATGCTCCAAAAAAGAGGAGATTGAGACCTTAAATGAAG
TGTCTCACAAACCAGGTGATCCAGGTTTTGTGGTCTTCCAAACACTTGTGGTCATTGTGTCCTTGATATTCATCTTTGTG
GTAGGACCTCGCCACTGGACAAACATTCTTGCGTACATACCAATCTGTTCCGTCATTGGAGCATTGTCAGTGTCCTGTGT
GAAGGGCCTGGGCATTGCTATCAAAGAGCTGTTTGCAGGAAAGTCCGTGCTGCAGCATCCTCTGGCCTGGATCCTTCTGC
TGAGCCTGGTTGTCTGTGTGAGCACACAGATTACCTGAACAGGAACCTGGACATCTTCAACACTTCCATTGTGACTCCAA
TATATTATGTATTCTTTACAACCTCTGTCTTAATGTATTCAGCTATTCTTTTCAAGGACTGGCAAGATATGCCTATTGGT
GATGTCATTGGTACTCCGAGAGGCTTCTTTACAATCATTGTGGAGATCATCCTGTTGCTTGCCTTTAAAGTTGTCAGCTT
T

Alignment

ORF - retro_ocun_1581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.14 %
• Parental protein coverage: 76.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KKKGLLRLARKGSMRAGQGGHAYLKEWLWWAGLLSMGAGEVANFAAYAFAPATLVTPLGALSVLVSAILS
          KKKG.LRLA.KGSMRA..GG.AYLKEWLWWAGL.S.G.GEVANFAAYAFAPA....P.GALSVL.SAILS
Retrocopy KKKGFLRLAEKGSMRAH*GGCAYLKEWLWWAGLQSRGVGEVANFAAYAFAPA----PIGALSVLISAILS

Parental  SYFLNERLNLHGKIGCLLSILGSTVM-VIHAPKE-EEIETLNEMSHKLGDPGFVVFATLVVIVSLIFIFV
          SYFLNER..LHGKI..LLSIL.STVM.VIHAPK..EEIETLNE.SHK.GDPGFVVF.TLVVIVSLIFIFV
Retrocopy SYFLNERPHLHGKIEYLLSILASTVM<VIHAPKK<EEIETLNEVSHKPGDPGFVVFQTLVVIVSLIFIFV

Parental  VGPRHGQTNILVYITICSVIGAFSVSCVKGLGIAIKELFAGKPVLRHPLAWILLLSLVV-CVSTQINYLN
          VGPRH..TNIL.YI.ICSVIGA.SVSCVKGLGIAIKELFAGK.VL.HPLAWI.LL...V.C......YLN
Retrocopy VGPRHW-TNILAYIPICSVIGALSVSCVKGLGIAIKELFAGKSVLQHPLAWI-LLLSLV<CLCEHTDYLN

Parental  RALDIFNTSIVTPIYYVFFTTSVLTCSAILFKEWQDMPVDDVIGTLSGFFTIIVGIFLLHAFKDVSF
          R.LDIFNTSIVTPIYYVFFTTSVL..SAILFK.WQDMP..DVIGT..GFFTIIV.I.LL.AFK.VSF
Retrocopy RNLDIFNTSIVTPIYYVFFTTSVLMYSAILFKDWQDMPIGDVIGTPRGFFTIIVEIILLLAFKVVSF

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	30.96 RPM
SRP017611_kidney	0.00 RPM	48.25 RPM
SRP017611_liver	0.00 RPM	15.18 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1581 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1581 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1581 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013824	1 retrocopy	retro_amel_1163,
Choloepus hoffmanni	ENSCHOG00000005553	1 retrocopy	retro_chof_9,
Callithrix jacchus	ENSCJAG00000005448	1 retrocopy	retro_cjac_1506,
Equus caballus	ENSECAG00000006379	1 retrocopy	retro_ecab_656,
Felis catus	ENSFCAG00000023073	1 retrocopy	retro_fcat_246,
Macaca mulatta	ENSMMUG00000003892	1 retrocopy	retro_mmul_1510,
Mus musculus	ENSMUSG00000030452	1 retrocopy	retro_mmus_3551,
Oryctolagus cuniculus	ENSOCUG00000010746	3 retrocopies	retro_ocun_1581 , retro_ocun_773, retro_ocun_809,
Ictidomys tridecemlineatus	ENSSTOG00000004003	3 retrocopies	retro_itri_1847, retro_itri_347, retro_itri_388,
Vicugna pacos	ENSVPAG00000000671	1 retrocopy	retro_vpac_285,