RetrogeneDB ID: retro_ocun_1574

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018701:7648806..7649252(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C15orf41
• Ensembl ID: ENSOCUG00000016099
• Aliases: None
• Description: chromosome 15 open reading frame 41 [Source:HGNC Symbol;Acc:26929]

Sequence

>retro_ocun_1574
GATGGAGTTCTAGCATATCAGGTCTGTCAGTGCACTGTGAACAACTGCTGTTGTGGACCACTGGTGGTCTGCATCAGACA
TGCCATTGGTCATGAGCATGAAGTCCTGCTGAGAGACTCGCGTCTAGGGAAAAATCTTTCTTTTCTGGATGAAGATCAGC
TCCGTGCAAAGGGTTATGACAAAACACCAGACTTTATTTTGCAAGTACCAGTTGCTGTGGAAGGGCACATCATTCACTAG
GTTGAAAGCGAAGCCTCATTTGGTGACGAATGTAGCCACCATGCCTACCTGCACGACCAGTCCCGGAGCTACGGGAACAG
ATCTGGGCCAGGCTTGGTCATCTGTTGGTACGGCTTTATCCAGGAGCTGGGCTGCAACCGGGAGAGGGGCATCCTGCTCA
AAGCCTATTTCCCGACCCACATCGTCACCTGTGCCACAGCACAGCT

Alignment

ORF - retro_ocun_1574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.0 %
• Parental protein coverage: 53.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGVLANQVYQCTVNDCCYGPLVDCIKHAIGHEHEVLLRDLLLEKNLSFLDEDQLRAKGYDKTPDFILQVP
          DGVLA.QV.QCTVN.CC.GPLV.CI.HAIGHEHEVLLRD..L.KNLSFLDEDQLRAKGYDKTPDFILQVP
Retrocopy DGVLAYQVCQCTVNNCCCGPLVVCIRHAIGHEHEVLLRDSRLGKNLSFLDEDQLRAKGYDKTPDFILQVP

Parental  VAVEGHIIHWIESKASFGDECSHHAYLHDQFWSYWNRFGPGLVIYWYGFIQELDCNRERGILLKACFPTD
          VAVEGHIIH..ES.ASFGDECSHHAYLHDQ..SY.NR.GPGLVI.WYGFIQEL.CNRERGILLKA.FPT.
Retrocopy VAVEGHIIH*VESEASFGDECSHHAYLHDQSRSYGNRSGPGLVICWYGFIQELGCNRERGILLKAYFPTH

Parental  IVT-LCHSTA
          IVT.LCHSTA
Retrocopy IVT<LCHSTA

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	3.42 RPM
SRP017611_kidney	0.00 RPM	3.85 RPM
SRP017611_liver	0.00 RPM	1.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1574 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1574 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014422	1 retrocopy	retro_dnov_2681,
Monodelphis domestica	ENSMODG00000001293	1 retrocopy	retro_mdom_1279,
Oryctolagus cuniculus	ENSOCUG00000016099	1 retrocopy	retro_ocun_1574 ,
Otolemur garnettii	ENSOGAG00000006789	1 retrocopy	retro_ogar_3224,