RetrogeneDB ID: retro_ocun_575

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:101757432..101757938(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000011406
• Aliases: None
• Description: None

Sequence

>retro_ocun_575
ATGTTGAGCTTGGAGATCAGCTCCTCCGGCTTCAGTCCGGAGACAAAATTGCTATCATCCCCCCATTAGTGGAGGCTAGT
GCATTTAAGCCATGTAGGAAAGATATGGATGATGTTGAAGAGAAACCTAAAGATACAATAAAATTCACTGCTGAGAAACT
TTCAGTGGATGAGATCTTGCAGTTGGTGATTTCTCCACCCTGCGGTGCAGTGTCCCTATTCGTAGGGAATACAAGAAATA
ACTTTGAAAGGAAGAAAGTCATTAGCTTAGAATATGAAGCTTATCTACCAATGGCGGAAAACGAGGTCAGAAAAATCTGT
AGTGACATCAGGCAGAAATGTCCAGTCACACACATAGCAGTGTTCCATCGACTTGGCTTAGTTCCGGTGTCAGAAGCAAG
CATAATCATTGCTGTGTCCTCAGCCCACAGGGCTGCATCCCTTGAAGCTGTGAGCTATGCCATTGATAATTTAAAAGCCA
AGGTACCCATATGGAAAAAGGAACTT

Alignment

ORF - retro_ocun_575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.94 %
• Parental protein coverage: 89.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSLEISSSSFSPETKLLLSP-PLVEASAFKPCRKDMDDVEEKPKDIIKFTAEKLSVDEVSQLVISPPCG
          M.SLEISSS.FSPETKLL.SP.PLVEASAFKPCRKDMDDVEEKPKD.IKFTAEKLSVDE..QLVISPPCG
Retrocopy MLSLEISSSGFSPETKLLSSP<PLVEASAFKPCRKDMDDVEEKPKDTIKFTAEKLSVDEILQLVISPPCG

Parental  AVSLFVGTTRNNFEGKKVISLEYEAYLPMAENEVRKICSDIRQKWPVTHIAVFHRLGLVPVSEASIIIAV
          AVSLFVG.TRNNFE.KKVISLEYEAYLPMAENEVRKICSDIRQK.PVTHIAVFHRLGLVPVSEASIIIAV
Retrocopy AVSLFVGNTRNNFERKKVISLEYEAYLPMAENEVRKICSDIRQKCPVTHIAVFHRLGLVPVSEASIIIAV

Parental  SSAHRAASLEAVSYAIDNLKARVPIWKKEM
          SSAHRAASLEAVSYAIDNLKA.VPIWKKE.
Retrocopy SSAHRAASLEAVSYAIDNLKAKVPIWKKEL

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	14.79 RPM
SRP017611_kidney	0.10 RPM	75.51 RPM
SRP017611_liver	0.00 RPM	39.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_575 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_575 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005380	1 retrocopy	retro_btau_487,
Cavia porcellus	ENSCPOG00000015752	2 retrocopies	retro_cpor_746, retro_cpor_748,
Macaca mulatta	ENSMMUG00000020449	1 retrocopy	retro_mmul_581,
Monodelphis domestica	ENSMODG00000019459	1 retrocopy	retro_mdom_1654,
Oryctolagus cuniculus	ENSOCUG00000011406	1 retrocopy	retro_ocun_575 ,
Otolemur garnettii	ENSOGAG00000011108	1 retrocopy	retro_ogar_2170,
Pteropus vampyrus	ENSPVAG00000010175	1 retrocopy	retro_pvam_633,
Ictidomys tridecemlineatus	ENSSTOG00000010607	1 retrocopy	retro_itri_241,
Tupaia belangeri	ENSTBEG00000008942	3 retrocopies	retro_tbel_1128, retro_tbel_216, retro_tbel_3310,
Tarsius syrichta	ENSTSYG00000001351	1 retrocopy	retro_tsyr_510,