RetrogeneDB ID: retro_cjac_496

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:201496218..201496543(+)
• Located in intron of: ENSCJAG00000004636

Retrocopy information

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

Parental gene information

• Parental gene symbol: JTB
• Ensembl ID: ENSCJAG00000009973
• Aliases: None
• Description: jumping translocation breakpoint [Source:HGNC Symbol;Acc:6201]

Sequence

>retro_cjac_496
GACAGAGTAAGCGCTGCCTCTGTGCCCTGAGAAGAACAGTGGTCCTAAGCACCTCAGATCTGTGTAGAACGGGGCACTCC
CCATTCTCATTTCTAGGCTAAAACCATCCCAGAGTGTGGCTTCACAGAGTCTGTGGAGAAAACCACATGCAGCTCACCTA
AGGAATGAGTTCAAAAGTGGTCTGCCCAGCTCTGACACAACCACGCCTATTCTGGAAATTCGAAGGGGCTGTTGGTTTAG
CCTTGATCTTTGACTGTCTTGTCATCAGTTGTCAGCTACAACTGGGCAAAAAGCTCTGGAAAACGTCTGGAGGCAAGTCG
AGTCC

Alignment

ORF - retro_cjac_496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.21 %
• Parental protein coverage: 74.83 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EKLSAVSTSNLPCWLVGEFVVSEECSPCSSFQAKTTPECGPTGYVEKITCSSSK-RNEFKS-CRSALMEQ
          ...SA.S......W........E...P.S.F.AKT.PECG.T..VEK.T..SS..RNEFKS....AL...
Retrocopy DRVSAASVP*EEQWS*APQICVERGTPHSHF*AKTIPECGFTESVEK-TTCSSP>RNEFKS>VCPALTQP

Parental  RLFWKFEGAVVCVALIFACLVIIRQRQLDR-KALEKVRKQIES
          RLFWKFEGAV...ALIF.CLVI..Q.QL...KALE.V..Q.ES
Retrocopy RLFWKFEGAV-GLALIFDCLVISCQLQLGK<KALENVWRQVES

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	0.11 RPM	9.61 RPM
SRP051959_heart	0.19 RPM	7.40 RPM
SRP051959_kidney	0.24 RPM	12.69 RPM
SRP051959_liver	0.09 RPM	17.72 RPM
SRP051959_lung	0.23 RPM	7.94 RPM
SRP051959_lymph_node	0.18 RPM	9.31 RPM
SRP051959_skeletal_muscle	0.17 RPM	15.09 RPM
SRP051959_spleen	0.21 RPM	11.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_496 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_496 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_496 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1886

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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,