RetrogeneDB ID: retro_ocun_470

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 11:42817879..42818317(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: JTB
• Ensembl ID: ENSOCUG00000011788
• Aliases: None
• Description: jumping translocation breakpoint [Source:HGNC Symbol;Acc:6201]

Sequence

>retro_ocun_470
ATGCCTGCGGGCGCGAGGAGTCGTGGCCTCCCCCAGGGCCACCGCCTTTGCTGGTTGCTCTGGGCTTTCACCTTAAAGCT
CTGCCAGGCAGAGGCTTCCGTGCCGGAGGAGAAACTGTCAGCGAGCACCTCGAATTTTCCATGCTGGCTGGTGGAAGAGT
TTGTGATGGCAGAGGAGTGCACTGCCTGTTCTAATTTCCAGACTAAAACCACCCCTGAGTGTGGCTCCACAGGGTACGTG
GAGAAAATCATGTGCAGCTCATCAAAAAGGAATGAGTTCAAAAGCTGCCGTTCAGCTCTGATGGAACAGCGTTTGTTCTG
GAAATTCAAAGGGGCTGTCTTGGGTGTGGCCTTGGTCTTCACTTTCCTCGTCATCATTTGACAGCGACAACTGGACAGAA
AGGCTCTGGAAAAGGTCCGGAAGCAAATCGTGTCCATA

Alignment

ORF - retro_ocun_470 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.84 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPAGARRRGLPQGRRLCWLLWAFTLKLCQAEASVPEEKLSASTSNLPCWLVEEFVVAEECTACSNFQTKT
          MPAGAR.RGLPQG.RLCWLLWAFTLKLCQAEASVPEEKLSASTSN.PCWLVEEFV.AEECTACSNFQTKT
Retrocopy MPAGARSRGLPQGHRLCWLLWAFTLKLCQAEASVPEEKLSASTSNFPCWLVEEFVMAEECTACSNFQTKT

Parental  TPECGSTGYVEKIMCSSSKRNEFKSCRSALMEQRLFWKFEGAVLGVALVFACLVIIRQRQLDRKALEKVR
          TPECGSTGYVEKIMCSSSKRNEFKSCRSALMEQRLFWKF.GAVLGVALVF..LVII.QRQLDRKALEKVR
Retrocopy TPECGSTGYVEKIMCSSSKRNEFKSCRSALMEQRLFWKFKGAVLGVALVFTFLVII*QRQLDRKALEKVR

Parental  KQIESI
          KQI.SI
Retrocopy KQIVSI

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	0.22 RPM	47.41 RPM
SRP017611_kidney	0.10 RPM	119.60 RPM
SRP017611_liver	0.08 RPM	9.56 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_470 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_470 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_470 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002520	1 retrocopy	retro_chof_1297,
Callithrix jacchus	ENSCJAG00000009973	1 retrocopy	retro_cjac_496,
Dasypus novemcinctus	ENSDNOG00000000740	1 retrocopy	retro_dnov_1095,
Echinops telfairi	ENSETEG00000008256	1 retrocopy	retro_etel_1340,
Felis catus	ENSFCAG00000012590	2 retrocopies	retro_fcat_1025, retro_fcat_1838,
Myotis lucifugus	ENSMLUG00000013299	1 retrocopy	retro_mluc_2225,
Oryctolagus cuniculus	ENSOCUG00000011788	1 retrocopy	retro_ocun_470 ,
Procavia capensis	ENSPCAG00000003210	1 retrocopy	retro_pcap_301,
Pongo abelii	ENSPPYG00000000791	1 retrocopy	retro_pabe_1886,
Sus scrofa	ENSSSCG00000006559	1 retrocopy	retro_sscr_687,
Tupaia belangeri	ENSTBEG00000012646	1 retrocopy	retro_tbel_762,