RetrogeneDB ID: retro_ocun_1186

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:28314772..28315182(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000024283
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: BTF3
• Ensembl ID: ENSOCUG00000024914
• Aliases: None
• Description: basic transcription factor 3 [Source:HGNC Symbol;Acc:1125]

Sequence

>retro_ocun_1186
AAGACGCGAGAAACTATCAGGAACCAGGAAAAACTCGCCACACTGCAGGCACAAGTGTGCGTTGGCGGGAAAGGAACTGC
TCGCAGAAAGAAGAAGGTGGTTCACAGAACAGCAACAGCTGGTGATAAAAAACGTCAGTTCTCCCTAAAGGAATTAGGGG
TAAACAATATCTCTGGTATTGAAGAGGTGAATCTGTTTGCAAACCAAGGAACAGTGATGCACTTCAACAACCCCAAAGTT
CAGGCTTCTCTGGCAGCAAACACCTTCACCATTACAGGCCTCGCTGAGACAAAGCAGCTGAGAGAAAGCTCCCCAGAACC
TTGAACCTGCTTGGCGCAGACAGCCTGACCAGCTTGAGGAGGCTGGCCGAAGCTCTGCCCACACAATCTATGGATGGAAA
AGCACCACTT

Alignment

ORF - retro_ocun_1186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.06 %
• Parental protein coverage: 73.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RMKETIMNQEKLAKLQAQVRIGGKGTARRKKKVVHRTATADDKKLQFSLKKLGVNNISGIEEVNMFTNQG
          ...ETI.NQEKLA.LQAQV..GGKGTARRKKKVVHRTATA.DKK.QFSLK.LGVNNISGIEEVN.F.NQG
Retrocopy KTRETIRNQEKLATLQAQVCVGGKGTARRKKKVVHRTATAGDKKRQFSLKELGVNNISGIEEVNLFANQG

Parental  TVIHFNNPKVQASLAANTFTITGHAETKQLTE-MLPSILNQLGADSLTSLRRLAEALPKQSVDGKAPL
          TV.HFNNPKVQASLAANTFTITG.AETKQL.E..LP..LN.LGADSLTSLRRLAEALP.QS.DGKAPL
Retrocopy TVMHFNNPKVQASLAANTFTITGLAETKQLRE<KLPRTLNLLGADSLTSLRRLAEALPTQSMDGKAPL

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	0.66 RPM	100.11 RPM
SRP017611_kidney	1.32 RPM	177.17 RPM
SRP017611_liver	0.31 RPM	61.27 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1186 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1186 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1186 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016600	4 retrocopies	retro_cjac_1454, retro_cjac_1673, retro_cjac_2640, retro_cjac_281,
Ciona savignyi	ENSCSAVG00000009653	1 retrocopy	retro_csav_25,
Echinops telfairi	ENSETEG00000017341	5 retrocopies	retro_etel_1216, retro_etel_1394, retro_etel_1997, retro_etel_405, retro_etel_960,
Gorilla gorilla	ENSGGOG00000000166	10 retrocopies	retro_ggor_1082, retro_ggor_1682, retro_ggor_1961, retro_ggor_2054, retro_ggor_2399, retro_ggor_2647, retro_ggor_2667, retro_ggor_548, retro_ggor_81, retro_ggor_946,
Monodelphis domestica	ENSMODG00000001762	3 retrocopies	retro_mdom_189, retro_mdom_454, retro_mdom_931,
Oryctolagus cuniculus	ENSOCUG00000001517	3 retrocopies	retro_ocun_1001, retro_ocun_1412, retro_ocun_1912,
Oryctolagus cuniculus	ENSOCUG00000024914	6 retrocopies	retro_ocun_1186 , retro_ocun_1299, retro_ocun_1364, retro_ocun_446, retro_ocun_857, retro_ocun_916,
Pongo abelii	ENSPPYG00000029576	14 retrocopies	retro_pabe_1154, retro_pabe_1477, retro_pabe_180, retro_pabe_1885, retro_pabe_1956, retro_pabe_2207, retro_pabe_2458, retro_pabe_2918, retro_pabe_2919, retro_pabe_2932, retro_pabe_3329, retro_pabe_3484, retro_pabe_558, retro_pabe_649,
Rattus norvegicus	ENSRNOG00000016912	9 retrocopies	retro_rnor_187, retro_rnor_194, retro_rnor_2121, retro_rnor_2520, retro_rnor_2990, retro_rnor_2991, retro_rnor_2999, retro_rnor_836, retro_rnor_953,