RetrogeneDB ID: retro_cjac_1901

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:37655953..37656862(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTBP1
• Ensembl ID: ENSCJAG00000020162
• Aliases: None
• Description: None

Sequence

>retro_cjac_1901
GCAGACACCGTGAGTGCCCAGCACGCCAAGCTGTCTCTGGACGGGCAGAACATCTACAACGCCTGCTGCACGCTGCGCAT
GGACTTCTCGAAGCTCACCAGCCTCAACGTCAAGTACAACAACGACAAGAGCCTTGACTACACGCGCGCAGATCTGCCCT
CTGGGGACAGCCAGCCCTCGCTGGACCAGACCATGGCTGCGACCTTCGGCCTTTCTGTTCCCAACGTCCACGGAGCCCTA
GCGCCCCTGGCCATCCCCTTGGCAGCGGCGGCAGCTGCGGCGGCAGGCCTGATCGCCATTCCGGGCCTGGTTGGGGCAGG
AAATTCTGTGTTGCTGGTCAGCAACCTCAACCCAGAGAGAGTCACACCCCAAAGCCTCTTTATTCTTTTCGGCGTCTACG
GCGATGTGCAGCACGTAAAGAGCCTGTTCAATAAGAAGGAGAATGCCCTGGTGCAGATGGTGGACAGCAACCAGGCCCAG
CTTGCCATGAGCCACCTGAACCGGCACAAGCTGTACCGGAAGCCCATCCACATCACACTCTCGAGGCACCAGAACGTGCA
GCTTCCCCGCCAGGGCCAGGAGGACCAGGGCCTGACCAAGGACTATGGCAACTCGCCCCTGCACCGCTTCAAGAAGCCAG
TATCCAAGAACTTCCAGAACATATTCCCACCCTCGGCCACCTAGCACCTCTCCAACATCCCGCCCGCAGTGTCCGAGGAA
GATCTCAAGGTCCTCTTCTCCAGCAATGGGGGCGTCGTCAAAGGATTCAAGTTCTTCCAGAAGGACCGCAAGATGGCGCT
GAACCAGATGGACTCCGTGGAGGAGGCGGTCCAGGCCCTCGTTCACCTGCACAACCACGACCTCGAGAAGAGCCACCACC
TGCGGGTCTCCTTCTCCAAGTCCACCATC

Alignment

ORF - retro_cjac_1901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.74 %
• Parental protein coverage: 58.44 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTMAAAFG
          AD.VSAQHAKLSLDGQNIYNACCTLR.DFSKLTSLNVKYNNDKS.DYTR.DLPSGDSQPSLDQTMAA.FG
Retrocopy ADTVSAQHAKLSLDGQNIYNACCTLRMDFSKLTSLNVKYNNDKSLDYTRADLPSGDSQPSLDQTMAATFG

Parental  KGLPGLSVPNVHGALAPLAIPSAAAAAAAAGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGD
          ...P...V......LA......AAAAA...G.IAIPGL.GAGNSVLLVSNLNPERVTPQSLFILFGVYGD
Retrocopy LSVP--NVHGALAPLAIPLAAAAAAAA---GLIAIPGLVGAGNSVLLVSNLNPERVTPQSLFILFGVYGD

Parental  VQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNS
          VQ.VK.LFNKKENALVQM.D.NQAQLAMSHLN.HKL..KPI.ITLS.HQNVQLPR.GQEDQGLTKDYGNS
Retrocopy VQHVKSLFNKKENALVQMVDSNQAQLAMSHLNRHKLYRKPIHITLSRHQNVQLPRQGQEDQGLTKDYGNS

Parental  PLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEE
          PLHRFKKP.SKNFQNIFPPSAT.HLSNIPP.VSEEDLKVLFSSNGGVVKGFKFFQKDRKMAL.QM.SVEE
Retrocopy PLHRFKKPVSKNFQNIFPPSAT*HLSNIPPAVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALNQMDSVEE

Parental  AVQALIDLHNHDLGESHHLRVSFSKSTI
          AVQAL..LHNHDL..SHHLRVSFSKSTI
Retrocopy AVQALVHLHNHDLEKSHHLRVSFSKSTI

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	0.00 RPM	22.39 RPM
SRP051959_heart	0.00 RPM	13.38 RPM
SRP051959_kidney	0.02 RPM	24.54 RPM
SRP051959_liver	0.02 RPM	13.91 RPM
SRP051959_lung	0.00 RPM	23.51 RPM
SRP051959_lymph_node	0.00 RPM	21.30 RPM
SRP051959_skeletal_muscle	0.02 RPM	6.60 RPM
SRP051959_spleen	0.00 RPM	19.54 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1901 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1901 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1901 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020162	1 retrocopy	retro_cjac_1901 ,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Dasypus novemcinctus	ENSDNOG00000000882	1 retrocopy	retro_dnov_982,
Equus caballus	ENSECAG00000018845	1 retrocopy	retro_ecab_330,
Echinops telfairi	ENSETEG00000006890	1 retrocopy	retro_etel_1573,
Homo sapiens	ENSG00000011304	1 retrocopy	retro_hsap_1354,
Gorilla gorilla	ENSGGOG00000005090	1 retrocopy	retro_ggor_1054,
Macropus eugenii	ENSMEUG00000006710	2 retrocopies	retro_meug_1447, retro_meug_67,
Myotis lucifugus	ENSMLUG00000003320	1 retrocopy	retro_mluc_755,
Nomascus leucogenys	ENSNLEG00000000864	1 retrocopy	retro_nleu_1834,
Pongo abelii	ENSPPYG00000009289	1 retrocopy	retro_pabe_1122,
Pan troglodytes	ENSPTRG00000010165	1 retrocopy	retro_ptro_928,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994, retro_rnor_2478,