RetrogeneDB ID: retro_ocun_860

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 16:23701641..23702577(+)
• Located in intron of: ENSOCUG00000015901

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000011872
• Aliases: None
• Description: None

Sequence

>retro_ocun_860
ATGAGTAGGGTCACCCCTTACATCGGCAGCAAGATCAGCCTCCTCTCCAAAGTGGAGATCCGCTATGAGGGCATCCTCTA
CACCAGTGACACCGAGAACTTCACGGTAGCCCTCGCCAAAGTTCGATCCTTTGGTACAGAAGACAGACCAACAGATCGTC
CAGTACCACCTCGAGATGAAGTCTTTGAATACATCATATTCCGTGGGAGTGATATTAAAGACCTCAGCGTTTGTGAGCCA
CTGAAACCACAGTGCTCTTTGCCTCAGGACTCCGCTATCGTGCAGTCATCACTAGGTTCATCTGCGTCTTCATTCCAGTC
AGTGGGTGCCTACAGACCTTTTGGCAGGATGCCGACATATAGTTAGTTCAGTCCAAGTTCATTAATCGGGCATCAGTTTG
GTATTGTTGGTGTTGCTGGAAGGTCTTGACATCATTTGGAACTGAAACATCAAACAGTGGTACTTTGTCCCAAAGCAGTG
CAGTTGGTTCTGCCTTTACACAGGATACAAGAGCTATAAAAACACAGTTATCTCAAGGTCGGTCAAGCCCTCAGTTAGAT
CCTTTGAGAAAAAAGCCCAACCATGGAACAAGCAGCACAGACCACCTTGGCCCACTTACCTGCTCCAGTATCTGTTGGGA
GAAGGAGCCCTGTATCAACCAGGTCTTTGCCATCTACCAGCCAAAAGGCAATAGAAAATCAAGAGCACAGGTGAGCTGAA
TTACACAAAGTTTCAAGACCAGAAAATGAGCAACTCAGAAATGATAACAAGTGACAAGTAGTTCCAGGTGCTCCTTCAGC
TCTGAGGAGAGGGCGTCAAGGTCATCGAGGTGGCAGAGGAAGGTTTGGTATCCGGAGCAATGGTCCAGTGAAATTTGAGA
AAGACTTTGACTTTGAAAGTGCAAATGCACAATTTAACAAGGAAGAGATTGACAGA

Alignment

ORF - retro_ocun_860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.49 %
• Parental protein coverage: 67.24 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSGGTPYIGSKISLISKAEIRYEGILYTIDTENSTVALAKVRSFGTEDRPTDRPIPPRDEVFEYIIFRGS
          MS..TPYIGSKISL.SK.EIRYEGILYT.DTEN.TVALAKVRSFGTEDRPTDRP.PPRDEVFEYIIFRGS
Retrocopy MSRVTPYIGSKISLLSKVEIRYEGILYTSDTENFTVALAKVRSFGTEDRPTDRPVPPRDEVFEYIIFRGS

Parental  DIKDLTVCEPPKPQCSLPQDPAIVQSSLGSSASSFQSVGSYGPFGRMPTYSQFSPSSLVGQQFGTVGVAG
          DIKDL.VCEP.KPQCSLPQD.AIVQSSLGSSASSFQSVG.Y.PFGRMPTYS.FSPSSL.G.QFG.VGVAG
Retrocopy DIKDLSVCEPLKPQCSLPQDSAIVQSSLGSSASSFQSVGAYRPFGRMPTYS*FSPSSLIGHQFGIVGVAG

Parental  SS-LTSFGTETSNSGTLSQSSAVGSAFTQDTRAIKTQLSQGRSSPQLDPLR-KSPTMEQAVQTASAHLPA
          .S.LTSFGTETSNSGTLSQSSAVGSAFTQDTRAIKTQLSQGRSSPQLDPLR.KSPTMEQA.QT..AHLPA
Retrocopy RS<LTSFGTETSNSGTLSQSSAVGSAFTQDTRAIKTQLSQGRSSPQLDPLR>KSPTMEQAAQTTLAHLPA

Parental  PAPVGRRSPVSTRPLPSTSQKAIENQEHRRAEVHKVSRPENEQLRNDNKRQVVPGAPSAPRRGRGGHRGG
          P..VGRRSPVSTR.LPSTSQKAIENQEHR.AE.HKVSRPENEQLRNDNK.QVVPGAPSA.RRGR.GHRGG
Retrocopy PVSVGRRSPVSTRSLPSTSQKAIENQEHR*AELHKVSRPENEQLRNDNK*QVVPGAPSALRRGRQGHRGG

Parental  RGRFGIRRDGPMKFEKDFDFESANAQFNKEEIDR
          RGRFGIR..GP.KFEKDFDFESANAQFNKEEIDR
Retrocopy RGRFGIRSNGPVKFEKDFDFESANAQFNKEEIDR

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	0.00 RPM	31.12 RPM
SRP017611_liver	0.15 RPM	14.95 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_860 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_860 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_860 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006555	1 retrocopy	retro_chof_1375,
Callithrix jacchus	ENSCJAG00000010360	5 retrocopies	retro_cjac_1582, retro_cjac_2625, retro_cjac_3201, retro_cjac_3327, retro_cjac_840,
Gorilla gorilla	ENSGGOG00000001762	1 retrocopy	retro_ggor_2378,
Microcebus murinus	ENSMICG00000011598	1 retrocopy	retro_mmur_1605,
Myotis lucifugus	ENSMLUG00000003368	1 retrocopy	retro_mluc_1793,
Macaca mulatta	ENSMMUG00000021614	2 retrocopies	retro_mmul_1386, retro_mmul_1860,
Nomascus leucogenys	ENSNLEG00000011713	4 retrocopies	retro_nleu_1299, retro_nleu_2544, retro_nleu_2580, retro_nleu_485,
Oryctolagus cuniculus	ENSOCUG00000011872	2 retrocopies	retro_ocun_193, retro_ocun_860 ,
Otolemur garnettii	ENSOGAG00000002492	2 retrocopies	retro_ogar_2586, retro_ogar_67,
Pongo abelii	ENSPPYG00000009832	2 retrocopies	retro_pabe_1693, retro_pabe_2906,
Pan troglodytes	ENSPTRG00000010813	3 retrocopies	retro_ptro_1343, retro_ptro_2389, retro_ptro_863,
Rattus norvegicus	ENSRNOG00000021133	1 retrocopy	retro_rnor_2397,
Ictidomys tridecemlineatus	ENSSTOG00000002785	1 retrocopy	retro_itri_170,