RetrogeneDB ID: retro_cjac_1284

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 14:53812291..53812729(-)
• Located in intron of: ENSCJAG00000010478

Retrocopy information

• Ensembl ID: ENSCJAG00000034686
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GLTP
• Ensembl ID: ENSCJAG00000034092
• Aliases: None
• Description: glycolipid transfer protein [Source:HGNC Symbol;Acc:24867]

Sequence

>retro_cjac_1284
ATGGCGCTGCTGGCCGAACACCTGCTGAAGCCGCTACCGGCGGACAAGCAGATCGAGACCGGGCCCTTCCTCGAGGCGGT
GTCCCACCTGCCGCCCTTCTTCGATTGCCTTGGGTCCCCAGTGTTTACTCCCATTAAGGCAGACATAAGCGGCAACATCA
CGAAAATCAAAGCGGTGTATGACACCAACCCAGCCAAGTTCCGGACCCTGCAGAACATCCTGGAGGTGGAGAAAGAAATG
TATGGAGCAGAGTGGCCCAAAGTTGGGGCCACACTGGCGCTGATGTGGCTGAAAAGGGGCCTCCGTTTCATCCAGGTCTT
CCTTCAGAGCATCTGCGACGGGGAGCGGAACGAGAACCACCCCAACCTCATCCGTGTCAACGCCACCAAGGCCTATGAGA
TGGCCCTCAAGAAGTACCACGGCTGGATCGTGCAGAGA

Alignment

ORF - retro_cjac_1284 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.63 %
• Parental protein coverage: 69.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALLAEHLLKPLPADKQIETGPFLEAVSHLPPFFDCLGSPVFTPIKADISGNITKIKAVYDTNPAKFRTL
          MALLAEHLLKPLPADKQIETGPFLEAVSHLPPFFDCLGSPVFTPIKADISGNITKIKAVYDTNPAKFRTL
Retrocopy MALLAEHLLKPLPADKQIETGPFLEAVSHLPPFFDCLGSPVFTPIKADISGNITKIKAVYDTNPAKFRTL

Parental  QNILEVEKEMYGAEWPKVGATLALMWLKRGLRFIQVFLQSICDGERDENHPNLIRVNATKAYEMALKKYH
          QNILEVEKEMYGAEWPKVGATLALMWLKRGLRFIQVFLQSICDGER.ENHPNLIRVNATKAYEMALKKYH
Retrocopy QNILEVEKEMYGAEWPKVGATLALMWLKRGLRFIQVFLQSICDGERNENHPNLIRVNATKAYEMALKKYH

Parental  GWIVQK
          GWIVQ.
Retrocopy GWIVQR

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	0.18 RPM	10.58 RPM
SRP051959_heart	0.04 RPM	3.86 RPM
SRP051959_kidney	0.02 RPM	9.72 RPM
SRP051959_liver	0.04 RPM	15.77 RPM
SRP051959_lung	0.15 RPM	8.38 RPM
SRP051959_lymph_node	0.16 RPM	6.03 RPM
SRP051959_skeletal_muscle	0.04 RPM	5.15 RPM
SRP051959_spleen	0.17 RPM	6.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1284 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1284 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1284 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034092	1 retrocopy	retro_cjac_1284 ,
Homo sapiens	ENSG00000139433	1 retrocopy	retro_hsap_755,
Myotis lucifugus	ENSMLUG00000012545	5 retrocopies	retro_mluc_1056, retro_mluc_1902, retro_mluc_2135, retro_mluc_2397, retro_mluc_658,
Macaca mulatta	ENSMMUG00000022761	1 retrocopy	retro_mmul_2261,
Pongo abelii	ENSPPYG00000004939	1 retrocopy	retro_pabe_28,
Pan troglodytes	ENSPTRG00000005431	1 retrocopy	retro_ptro_41,