RetrogeneDB ID: retro_ocun_118

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018717:2257627..2258485(-)
• Located in intron of: ENSOCUG00000026803

Retrocopy information

• Ensembl ID: ENSOCUG00000023781
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000014589
• Aliases: None
• Description: None

Sequence

>retro_ocun_118
ATGCCAGCAGCAACTGTAGATCATAGCCAAAGAATTTGTGAAGTTTGGGCTTGCAACCTGGATGAAGAGATGAAGAAAAT
TCGTCAAGTTATCCGAAAATACAATTACGTTGCTATGGACACTGAGTTTCCAGGTGTGGTTGCAAGACCTATTGGCGAAT
TCAGGAGCAATGCTGACTATCAGTACCAACTGTTGCGGTGTAATGTAGACTTGTTAAAGATAATTCAGCTAGGACTGACC
TTTATGAATGAACAAGGAGAATACCCTCCAGGAACTTCAACTTGGCAGTTTAATTTTAAATTTAATTTGACGGAGGACAT
GTATGCCCAGGACTCCATAGAGCTGCTAACAACATCTGGTATCCAATTTAAAAAACATGAGGAGGAAGGAATTGAGACCC
AGTACTTTGCAGAACTTCTTATGACTTCTGGAGTGGTCCTCTGTGAGGGGGTCAAATGGTTATCATTTCATAGTGGTTAT
GACTTTGGCTATTTAATCAAAATCCTGACAAACTCCAATTTGCCCGAAGAAGAACTTGACTTCTTTGAGATCCTTCGCTT
GTTTTTTCCTGTCATTTATGATGTGAAGTACCTCATGAAGAGCTGCAAAAATCTTAAAGGTGGATTGCAGGAAGTTGCTG
AACAGTTAGAGCTGGAACGGATAGGACCACAACATCAGGCAGGATCTGATTCATTACTCACAGGAATGGCCTTTTTCAAA
ATGAGAGAAATGTTCTTTGAAGATCATATTGATGATGCCAAATATTGTGGTCATTTGTATGGCCTTGGTTCTGGTTCATC
CTATGTACAGAATGGCACAGGGAATGCATATGAAGAGGAAGCCAACAAGCAGTCATGA

Alignment

ORF - retro_ocun_118 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MPAATVDHSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVD
          MPAATVDHSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVD
Retrocopy MPAATVDHSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVD

Parental  LLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELL
          LLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELL
Retrocopy LLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELL

Parental  MTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQ
          MTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQ
Retrocopy MTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQ

Parental  EVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYCGHLYGLGSGSSYVQNGTGNAYEEE
          EVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYCGHLYGLGSGSSYVQNGTGNAYEEE
Retrocopy EVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYCGHLYGLGSGSSYVQNGTGNAYEEE

Parental  ANKQS
          ANKQS
Retrocopy ANKQS

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	3.64 RPM	8.89 RPM
SRP017611_kidney	3.14 RPM	7.30 RPM
SRP017611_liver	1.77 RPM	4.55 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_118 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_118 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_118 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000677	4 retrocopies	retro_chof_1431, retro_chof_1581, retro_chof_822, retro_chof_963,
Callithrix jacchus	ENSCJAG00000011795	1 retrocopy	retro_cjac_720,
Felis catus	ENSFCAG00000000591	1 retrocopy	retro_fcat_1889,
Homo sapiens	ENSG00000198791	2 retrocopies	retro_hsap_211, retro_hsap_4851,
Gorilla gorilla	ENSGGOG00000015762	2 retrocopies	retro_ggor_282, retro_ggor_3027,
Macaca mulatta	ENSMMUG00000001873	1 retrocopy	retro_mmul_2592,
Monodelphis domestica	ENSMODG00000019055	2 retrocopies	retro_mdom_1898, retro_mdom_802,
Mustela putorius furo	ENSMPUG00000017972	1 retrocopy	retro_mputfur_1596,
Nomascus leucogenys	ENSNLEG00000002489	2 retrocopies	retro_nleu_1860, retro_nleu_2373,
Oryctolagus cuniculus	ENSOCUG00000014589	1 retrocopy	retro_ocun_118 ,
Otolemur garnettii	ENSOGAG00000006324	2 retrocopies	retro_ogar_1883, retro_ogar_505,
Pongo abelii	ENSPPYG00000018385	2 retrocopies	retro_pabe_3771, retro_pabe_428,
Sarcophilus harrisii	ENSSHAG00000011828	2 retrocopies	retro_shar_103, retro_shar_631,
Ictidomys tridecemlineatus	ENSSTOG00000009175	2 retrocopies	retro_itri_1729, retro_itri_1730,