RetrogeneDB ID: retro_ocun_342

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:15214104..15214648(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023271
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000015632
• Aliases: None
• Description: None

Sequence

>retro_ocun_342
CCTTGGGATTCGGAGGATGTAAAAGGACTTAGAATATCAGCTATTCGGGATAACAATCCAGTGGTGGGGTAGAGAATGAA
TTGATGTATGACATTCCTTTGGAACTTCCTGCTGAAGCTCAGTCAAAAGATTTTCTGATTCCTATCGGAAAAGCCAAAAT
AGAATGCCAAGGGACACACGTAACCGTGGTTGCCCATTCGAGACTTGTGGGCCACTGTTTAGAAGCTGGGACATTATTTT
CTAAAGAGGGAGTTGAATGTGAGGTCACAGGTCTGCGTACCATCAGACCAATGGATGTTGAAGCCACAGAAGGCAGCGCC
ATGAAAACAAGTCATCTGGTAACAGTGGAAGGAGGCTGGCCACAGTTTGGAGATGGAGCTGAAAGTTGTGCTAGTGTCAT
GGAAGGCCCTGCACTCAATGTCCTGGATGCACCTGCTGTCTGTGTCACTGGTACTGACCTCCCTCGGCCGTATACAGATT
CTTGAAGACATCTATACCTCAGGTCAAAGACATCATACTTGCAATAAAGAAAACATTAGACATC

Alignment

ORF - retro_ocun_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.68 %
• Parental protein coverage: 50.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PWNSEDAKGLIKSAIRDNNPVVV-LENELMYGVPFELPAEAQSKDFLIPIGKAKIERQGTHITVVAHSRP
          PW.SED.KGL..SAIRDNNPVV...ENELMY..P.ELPAEAQSKDFLIPIGKAKIE.QGTH.TVVAHSR.
Retrocopy PWDSEDVKGLRISAIRDNNPVVG<VENELMYDIPLELPAEAQSKDFLIPIGKAKIECQGTHVTVVAHSRL

Parental  VGHCLEAATVLSKEGVECEVINLRTIRPMDIETIEASVMKTNHLVTVEGGWPQFGVGAEICARIMEGPAF
          VGHCLEA.T..SKEGVECEV..LRTIRPMD.E..E.S.MKT.HLVTVEGGWPQFG.GAE.CA..MEGPA.
Retrocopy VGHCLEAGTLFSKEGVECEVTGLRTIRPMDVEATEGSAMKTSHLVTVEGGWPQFGDGAESCASVMEGPAL

Parental  NFLDAPAVRVTGADV-PMPYAKILEDNSIPQVKDIIFAIKKTLNI
          N.LDAPAV.VTG.D..P......L...SIPQVKDII.AIKKTL.I
Retrocopy NVLDAPAVCVTGTDL<PSAVYRFLK-TSIPQVKDIILAIKKTLDI

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	85.21 RPM
SRP017611_kidney	0.00 RPM	123.45 RPM
SRP017611_liver	0.00 RPM	21.27 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_342 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_342 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_342 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021724	1 retrocopy	retro_btau_596,
Canis familiaris	ENSCAFG00000007340	2 retrocopies	retro_cfam_1215, retro_cfam_2031,
Callithrix jacchus	ENSCJAG00000019739	1 retrocopy	retro_cjac_3875,
Dasypus novemcinctus	ENSDNOG00000006937	1 retrocopy	retro_dnov_1090,
Monodelphis domestica	ENSMODG00000002398	1 retrocopy	retro_mdom_614,
Mus musculus	ENSMUSG00000021748	1 retrocopy	retro_mmus_290,
Oryctolagus cuniculus	ENSOCUG00000015632	1 retrocopy	retro_ocun_342 ,
Procavia capensis	ENSPCAG00000016595	1 retrocopy	retro_pcap_261,
Sarcophilus harrisii	ENSSHAG00000008480	1 retrocopy	retro_shar_5,
Ictidomys tridecemlineatus	ENSSTOG00000019553	2 retrocopies	retro_itri_1349, retro_itri_249,
Tupaia belangeri	ENSTBEG00000016148	2 retrocopies	retro_tbel_1651, retro_tbel_3170,