RetrogeneDB ID: retro_ocun_496

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 12:22033281..22033598(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL1
• Ensembl ID: ENSOCUG00000016834
• Aliases: None
• Description: GABA(A) receptor-associated protein like 1 [Source:HGNC Symbol;Acc:4068]

Sequence

>retro_ocun_496
ATCATGAAGTTCCAGTATAAGGAGGACCATCCTCTTGAGTACTGGAAAAAGAAAGGAGAAAAGATCCAGAAGAAATATCC
GGACAGGGTCCCTGTAATTGTGGAGAAGGCACCTAAAGCCAGAGTACCAGATCTGGAGAAGAGGAAGTACCTACTGCCTT
CTGGCCTCACTATTGGCCAATTCTACATCTTACTTTGGAGGGGATCCACTTGAGACTTGAGGACGTCTTATTCTTCTTTG
TCAGCAACACTATCCCTTCCACTAATGCCACCTGAGACCAGCTGTATGAGGACAACCATGAGGAAAACTATTTTGTA

Alignment

ORF - retro_ocun_496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.5 %
• Parental protein coverage: 87.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IMKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLI-RKRI
          IMKFQYKEDHP.EY.KK.GEKI.KKYPDRVPVIVEKAPKARVPDL.KRKYL.PS.LT.GQFY.L.....I
Retrocopy IMKFQYKEDHPLEYWKKKGEKIQKKYPDRVPVIVEKAPKARVPDLEKRKYLLPSGLTIGQFYILL<LEGI

Parental  HLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFL
          HLR.ED.LFFFV.NTIP.T.AT..QLYEDNHEE.YF.
Retrocopy HLRLEDVLFFFVSNTIPSTNAT*DQLYEDNHEENYFV

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	174.78 RPM
SRP017611_kidney	0.10 RPM	234.13 RPM
SRP017611_liver	0.00 RPM	56.26 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_496 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_496 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_496 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001218	1 retrocopy	retro_chof_329,
Cavia porcellus	ENSCPOG00000006718	1 retrocopy	retro_cpor_232,
Homo sapiens	ENSG00000139112	1 retrocopy	retro_hsap_60,
Macaca mulatta	ENSMMUG00000002197	1 retrocopy	retro_mmul_2235,
Oryctolagus cuniculus	ENSOCUG00000006997	1 retrocopy	retro_ocun_311,
Oryctolagus cuniculus	ENSOCUG00000016834	3 retrocopies	retro_ocun_1380, retro_ocun_496 , retro_ocun_697,
Oryctolagus cuniculus	ENSOCUG00000022970	4 retrocopies	retro_ocun_1155, retro_ocun_572, retro_ocun_731, retro_ocun_784,
Sarcophilus harrisii	ENSSHAG00000007434	1 retrocopy	retro_shar_82,
Ictidomys tridecemlineatus	ENSSTOG00000002246	1 retrocopy	retro_itri_391,
Tarsius syrichta	ENSTSYG00000005307	19 retrocopies	retro_tsyr_1045, retro_tsyr_1070, retro_tsyr_1101, retro_tsyr_1137, retro_tsyr_1308, retro_tsyr_1413, retro_tsyr_1467, retro_tsyr_1481, retro_tsyr_1671, retro_tsyr_1765, retro_tsyr_1800, retro_tsyr_234, retro_tsyr_573, retro_tsyr_761, retro_tsyr_796, retro_tsyr_832, retro_tsyr_864, retro_tsyr_978, retro_tsyr_999,
Tursiops truncatus	ENSTTRG00000009099	3 retrocopies	retro_ttru_1451, retro_ttru_1563, retro_ttru_1629,