RetrogeneDB ID: retro_ocun_1300

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:48588271..48588724(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000021967
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000017371
• Aliases: None
• Description: None

Sequence

>retro_ocun_1300
ATGTGCATCTTCACTGAAGACCAGGCCACAGAATTCAAGGAGGCCTTCCCGCTTTTTGACTGGACAGGTGATTGTAAGAC
CCTGTACAGCCAGTGTGGGGATGTGATAAGGGCTTTGGGCCAGAACCCCACCAATGCCAAGGTGCTCAAAGTCCTGGGGA
ACCCCAGGAGTGATGAGATGAATGTTAAGGTGCTGGACCTTGAGTACTTCCTGCCAATGCTGCAGATTGTGACCAAGAGC
AAGGACCAGGGAATCTACAAGGATTATGTTGAAGGCCTTTGGATGTTTGACAAGGAAAGGAATGGCACTAGCATGGGTGC
TGAAATCTATCATGTCCTTGTCACATGGGGTGAGAAGATGACAGAGGAAGAAGTAGAGATGCTAGTGGCAGGGCACAAAG
GCAGCAGTGGTCATACCAACTATAAAGAGCTTATCCGTATGATGCCAAGTGGC

Alignment

ORF - retro_ocun_1300 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCDFTEDQTAEFKEAFQLFDRTGDGKILYSQCGDVMRALGQNPTNAEVLKVLGNPKSDEMNVKVLDFEHF
          MC.FTEDQ..EFKEAF.LFD.TGD.K.LYSQCGDV.RALGQNPTNA.VLKVLGNP.SDEMNVKVLD.E.F
Retrocopy MCIFTEDQATEFKEAFPLFDWTGDCKTLYSQCGDVIRALGQNPTNAKVLKVLGNPRSDEMNVKVLDLEYF

Parental  LPMLQTVAKNKDQGTYEDYVEGLRVFDKEGNGTVMGAEIRHVLVTLGEKMTEEEVEMLVAGHEDSNGCIN
          LPMLQ.V.K.KDQG.Y.DYVEGL..FDKE.NGT.MGAEI.HVLVT.GEKMTEEEVEMLVAGH..S.G..N
Retrocopy LPMLQIVTKSKDQGIYKDYVEGLWMFDKERNGTSMGAEIYHVLVTWGEKMTEEEVEMLVAGHKGSSGHTN

Parental  YEELVRMVLNG
          Y.EL.RM...G
Retrocopy YKELIRMMPSG

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	231.63 RPM
SRP017611_kidney	0.00 RPM	393.97 RPM
SRP017611_liver	0.00 RPM	68.75 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1300 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1300 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1300 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000092841	2 retrocopies	retro_hsap_1786, retro_hsap_2533,
Macropus eugenii	ENSMEUG00000001272	1 retrocopy	retro_meug_2172,
Macaca mulatta	ENSMMUG00000031838	6 retrocopies	retro_mmul_1633, retro_mmul_1663, retro_mmul_211, retro_mmul_2221, retro_mmul_2410, retro_mmul_96,
Mus musculus	ENSMUSG00000090841	7 retrocopies	retro_mmus_1281, retro_mmus_1504, retro_mmus_2328, retro_mmus_3231, retro_mmus_3333, retro_mmus_3358, retro_mmus_434,
Nomascus leucogenys	ENSNLEG00000000205	2 retrocopies	retro_nleu_2736, retro_nleu_779,
Oryctolagus cuniculus	ENSOCUG00000017368	1 retrocopy	retro_ocun_374,
Oryctolagus cuniculus	ENSOCUG00000017371	1 retrocopy	retro_ocun_1300 ,
Otolemur garnettii	ENSOGAG00000034596	1 retrocopy	retro_ogar_2549,
Pongo abelii	ENSPPYG00000004647	3 retrocopies	retro_pabe_1467, retro_pabe_1864, retro_pabe_538,
Pan troglodytes	ENSPTRG00000005080	2 retrocopies	retro_ptro_1196, retro_ptro_1476,
Sarcophilus harrisii	ENSSHAG00000004472	6 retrocopies	retro_shar_137, retro_shar_318, retro_shar_452, retro_shar_510, retro_shar_719, retro_shar_765,
Sus scrofa	ENSSSCG00000025467	1 retrocopy	retro_sscr_829,
Ictidomys tridecemlineatus	ENSSTOG00000023318	1 retrocopy	retro_itri_1478,
Tupaia belangeri	ENSTBEG00000000485	8 retrocopies	retro_tbel_130, retro_tbel_1715, retro_tbel_2980, retro_tbel_332, retro_tbel_3515, retro_tbel_3545, retro_tbel_3707, retro_tbel_4075,