RetrogeneDB ID: retro_ocun_1449

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:49121621..49122349(-)
• Located in intron of: ENSOCUG00000015173

Retrocopy information

• Ensembl ID: ENSOCUG00000024639
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CLIC1
• Ensembl ID: ENSOCUG00000022545
• Aliases: None
• Description: chloride intracellular channel 1 (CLIC1), mRNA [Source:RefSeq mRNA;Acc:NM_001082111]

Sequence

>retro_ocun_1449
ATGGCTGAAGAGCAACCACAGGTCGAACTGTTCGTGAAGTCTGGCAGTGATGGGGCCAAGATCAGAAGCTGCCCCTTCTC
CCAGAGATTGTTCATGGTACTATGGGCTCAAGGGAGTCACCTTCAATGTCACCACTGTTGACACCAAGAAATGGACGGAG
ACAGTGCAGAAGCTGTGCCCAGGAGGGCAGCTCCCCTTCCTGTTGTATGGCACTGAAGTCCACACAGACATCAACAAGAA
TCGAGGAATTTCTGGAGGCAGTGCTGTGCCCTCCCAAGTACCCAGAGCTGGCAGCTCTGAACCCTGAGTCCAACACGGCT
GGTGTAGACATATTTGCCAAATTTTCTGCCTACATCAAGAATTCAAACCCAGTGCTCAATGACAATCTGGAGAAGGGGCT
CCTGAAAGCCTTGAAGATTTTAGACAATTACCTGACCCCCCCCCCCGCTCCCGAAGAAGTGGATGAGACCAGTGCTGAAG
ATGAGGGTATCTCTCAGAGGAAGTTTCTGGATGGCAATGAGCTCACCCTGGCTGACTGTAACCTGTTGCCAAAGCTGCAC
ATAGTACAGGTGGTGTGTAAGAAATACCGGGGATTCACCATCCCAGAGGTGTTCCAAGGAATGCACCGGTACTTGAGCAA
CGCCTATGCTCGCGAAGAATTTGTCTCCACCTGTCCAGATGATGAAGAGATTGAACTTGCCTGCGACCAAATGGCCAAGG
CCCTGAAA

Alignment

ORF - retro_ocun_1449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEEQPQVELFVKAGSDGAKIGNCPFSQRLFMVLW-LKGVTFNVTTVDTKRRTETVQKLCPGGQLPFLLY
          MAEEQPQVELFVK.GSDGAKI..CPFSQRLFMVLW.LKGVTFNVTTVDTK..TETVQKLCPGGQLPFLLY
Retrocopy MAEEQPQVELFVKSGSDGAKIRSCPFSQRLFMVLW>LKGVTFNVTTVDTKKWTETVQKLCPGGQLPFLLY

Parental  GTEVHTDTNK-IEEFLEAVLCPPRYPKLAALNPESNTAGVDIFAKFSAYIKNSNPALNDNLEKGLLKALK
          GTEVHTD.NK.IEEFLEAVLCPP.YP.LAALNPESNTAGVDIFAKFSAYIKNSNP.LNDNLEKGLLKALK
Retrocopy GTEVHTDINK>IEEFLEAVLCPPKYPELAALNPESNTAGVDIFAKFSAYIKNSNPVLNDNLEKGLLKALK

Parental  ILDNYLTSP-LPEEVDETSAEDEGISQRKFLDGNELTLADCNLLPKLHIVQVVCKKYRGFTIPEVFRGVH
          ILDNYLT.P..PEEVDETSAEDEGISQRKFLDGNELTLADCNLLPKLHIVQVVCKKYRGFTIPEVF.G.H
Retrocopy ILDNYLTPPPAPEEVDETSAEDEGISQRKFLDGNELTLADCNLLPKLHIVQVVCKKYRGFTIPEVFQGMH

Parental  RYLSNAYAREEFASTCPDDEEIELAYEQVAKALK
          RYLSNAYAREEF.STCPDDEEIELA..Q.AKALK
Retrocopy RYLSNAYAREEFVSTCPDDEEIELACDQMAKALK

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	0.17 RPM	19.81 RPM
SRP017611_kidney	0.00 RPM	79.87 RPM
SRP017611_liver	0.15 RPM	31.83 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1449 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1449 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1449 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000621	2 retrocopies	retro_cfam_481, retro_cfam_525,
Callithrix jacchus	ENSCJAG00000002788	1 retrocopy	retro_cjac_2972,
Dipodomys ordii	ENSDORG00000016424	3 retrocopies	retro_dord_506, retro_dord_524, retro_dord_550,
Felis catus	ENSFCAG00000019049	1 retrocopy	retro_fcat_1301,
Gorilla gorilla	ENSGGOG00000011331	1 retrocopy	retro_ggor_2153,
Macropus eugenii	ENSMEUG00000015201	1 retrocopy	retro_meug_254,
Macaca mulatta	ENSMMUG00000029827	3 retrocopies	retro_mmul_1269, retro_mmul_290, retro_mmul_902,
Monodelphis domestica	ENSMODG00000015240	1 retrocopy	retro_mdom_1166,
Nomascus leucogenys	ENSNLEG00000006264	3 retrocopies	retro_nleu_1296, retro_nleu_24, retro_nleu_2894,
Oryctolagus cuniculus	ENSOCUG00000022545	1 retrocopy	retro_ocun_1449 ,
Otolemur garnettii	ENSOGAG00000031840	4 retrocopies	retro_ogar_2402, retro_ogar_3273, retro_ogar_407, retro_ogar_982,
Procavia capensis	ENSPCAG00000013268	1 retrocopy	retro_pcap_30,
Pongo abelii	ENSPPYG00000016456	2 retrocopies	retro_pabe_1514, retro_pabe_886,
Pan troglodytes	ENSPTRG00000017982	2 retrocopies	retro_ptro_1238, retro_ptro_724,
Sarcophilus harrisii	ENSSHAG00000006493	1 retrocopy	retro_shar_28,
Tarsius syrichta	ENSTSYG00000001540	2 retrocopies	retro_tsyr_1452, retro_tsyr_722,