RetrogeneDB ID: retro_cjac_3820

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284785.1:20880..21225(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000022353
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GABARAP
• Ensembl ID: ENSCJAG00000016655
• Aliases: None
• Description: GABA(A) receptor-associated protein [Source:HGNC Symbol;Acc:4067]

Sequence

>retro_cjac_3820
ATAAAGTTCGTGTACAAAGAAGAGCATCCCTTTGAGAAGCTCCGCTCTGAGGGCCAGAAGAACCTAAAGAAATACCCGGA
CCGGGTGCAGATGATAGTAGAAAAAGCTCCCAAAGTTCGGATAGGAGACCTGGACAAAAAGAAATACCTGGTGCCTTCTG
TTCTCACAGTTGGTCAGTTCTACTTCTTGATCCGGAAGCGAATTCATCTCCGATCTGAGGATGCCTTGTTTTTCTTTGTC
AACAATGTAATTCCACCCACCACGATGGGTCAACTTTACCAGGAACATCATGAAGAAGAGTTCTTTCTGTACATTGCCTA
TAGTGACGAAAGTGTCTACGGTCTG

Alignment

ORF - retro_cjac_3820 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHL
          .KFVYKEEHPFEK.RSEG.K..KKYPDRV..IVEKAPK.RIGDLDKKKYLVPS.LTVGQFYFLIRKRIHL
Retrocopy IKFVYKEEHPFEKLRSEGQKNLKKYPDRVQMIVEKAPKVRIGDLDKKKYLVPSVLTVGQFYFLIRKRIHL

Parental  RAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL
          R.EDALFFFVNNVIPPT..TMGQLYQEHHEE.FFLYIAYSDESVYGL
Retrocopy RSEDALFFFVNNVIPPT--TMGQLYQEHHEEEFFLYIAYSDESVYGL

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
SRP051959_colon	0.02 RPM	11.00 RPM
SRP051959_heart	0.00 RPM	17.10 RPM
SRP051959_kidney	0.00 RPM	19.44 RPM
SRP051959_liver	0.00 RPM	14.06 RPM
SRP051959_lung	0.02 RPM	15.26 RPM
SRP051959_lymph_node	0.02 RPM	10.23 RPM
SRP051959_skeletal_muscle	0.00 RPM	28.48 RPM
SRP051959_spleen	0.02 RPM	18.57 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3820 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3820 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3820 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000012473	1 retrocopy	retro_cint_25,
Callithrix jacchus	ENSCJAG00000004473	3 retrocopies	retro_cjac_1114, retro_cjac_1519, retro_cjac_779,
Callithrix jacchus	ENSCJAG00000014253	1 retrocopy	retro_cjac_146,
Callithrix jacchus	ENSCJAG00000016655	2 retrocopies	retro_cjac_2851, retro_cjac_3820 ,
Gorilla gorilla	ENSGGOG00000013770	1 retrocopy	retro_ggor_821,
Loxodonta africana	ENSLAFG00000000744	1 retrocopy	retro_lafr_61,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
Mus musculus	ENSMUSG00000018567	1 retrocopy	retro_mmus_3107,
Nomascus leucogenys	ENSNLEG00000008049	2 retrocopies	retro_nleu_1670, retro_nleu_4,
Oryctolagus cuniculus	ENSOCUG00000006997	1 retrocopy	retro_ocun_311,
Pongo abelii	ENSPPYG00000007901	1 retrocopy	retro_pabe_122,
Pan troglodytes	ENSPTRG00000034115	1 retrocopy	retro_ptro_60,
Rattus norvegicus	ENSRNOG00000017417	2 retrocopies	retro_rnor_1818, retro_rnor_2093,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163,
Drosophila melanogaster	FBgn0052672	1 retrocopy	retro_dmel_23,