RetrogeneDB ID: retro_cjac_1175

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:110406625..110407399(-)
• Located in intron of: ENSCJAG00000003126

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNF8
• Ensembl ID: ENSCJAG00000007322
• Aliases: None
• Description: SNF8, ESCRT-II complex subunit [Source:HGNC Symbol;Acc:17028]

Sequence

>retro_cjac_1175
ATGCACCGCTGTGGGGTGGGAGCTGGCGCCTTCATGAAGCACTAACTTTCAGAGGCCAAGTATAGGGAGCGAGGGACGGT
CTTGGCTGAGGACCAACTAGCCCAGATGTCAAAGCAGTTGGACATGTTCAAGACAAACCTGGAAGAATTTGCCAGCAAGC
ACAAGCAGGAGATCCAGAAGAATCCTGAGTTCCACGTGCAGTTCTAGGACGTGTTTGCCACCATTGGTGTGGATCCTCTA
GTCTCTGGAAAAGGATTTTGGTCTGAGATGCTGGGCCTGGGGGACTTCTATTATGAACTAGGTGTCCAAATTACCGAAGT
GTGCTTGGCACTGAATCATCGGAATGGAGGTCTGATAACTCTGGAGGAACTACATCAACAGGTGTTGAAGTGAAGGGGCA
AGTTCGCCCAGGTTGTCAGTCAAGGCGACCTGATCAGGGCCATCAAGAAACTAAAGGCACTTGGGACTGGCTTCTGCATC
ATCCCTGTGGGCGGCACTTACCTCATTCAGTCTGTTCCAGCTGAGCTCAATATGCATCACACCGTGGTGCTGCAGCTGGC
AGAGAAAAATGTCTACGTGACTGTCAGTGAGATCAGAGCCAGTCTTAAATGGGAGACTGAGCGAGCATGGCAAGTGCTGG
AACACCTGCTGAGGGAAGGGCTGGCGTGGCTGGACTTGCAGGCACCAGGGGAGGCCCAGTACTGGCTGCCAGCTTTCTTC
ACTGACCTTTACTCCCAGGAGATTACAGCTGAGGAGGCCAGAGAAACCCTTCCC

Alignment

ORF - retro_cjac_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.46 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHRRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQD
          MHR.GVGAGA..K..L.EAKY.ERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEI.KNPEF.VQF.D
Retrocopy MHRCGVGAGAFMKH*LSEAKYRERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIQKNPEFHVQF*D

Parental  MCATIGVDPLASFSLFFKKMF---NFYYELGVQIIEVCLALKHRNGEQKITSHTHCKLFSGRGPCLFTDV
          ..ATIGVDPL.S...F...M.....FYYELGVQI.EVCLAL.HRNG........H......RG...F..V
Retrocopy VFATIGVDPLVSGKGFWSEMLGLGDFYYELGVQITEVCLALNHRNGGLITLEELHQQVLK*RGK--FAQV

Parental  V-EDDLIRAIKKLKALGTGFCIIPVGGTYLIQSVPAELNMDHTVVLQLAEKNGYVTVSEIKASLKWETER
          V...DLIRAIKKLKALGTGFCIIPVGGTYLIQSVPAELNM.HTVVLQLAEKN.YVTVSEI.ASLKWETER
Retrocopy VSQGDLIRAIKKLKALGTGFCIIPVGGTYLIQSVPAELNMHHTVVLQLAEKNVYVTVSEIRASLKWETER

Parental  ARQVLEHLLKEGLAWLDLQAPGEAHYWLPALFTDLYSQEITAEEAREALP
          A.QVLEHLL.EGLAWLDLQAPGEA.YWLPA.FTDLYSQEITAEEARE.LP
Retrocopy AWQVLEHLLREGLAWLDLQAPGEAQYWLPAFFTDLYSQEITAEEARETLP

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	1.18 RPM	7.57 RPM
SRP051959_heart	0.77 RPM	7.24 RPM
SRP051959_kidney	1.53 RPM	9.70 RPM
SRP051959_liver	0.97 RPM	7.06 RPM
SRP051959_lung	0.76 RPM	8.30 RPM
SRP051959_lymph_node	0.62 RPM	9.73 RPM
SRP051959_skeletal_muscle	0.90 RPM	7.34 RPM
SRP051959_spleen	0.99 RPM	8.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1175 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1175 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1175 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005062	1 retrocopy	retro_amel_164,
Canis familiaris	ENSCAFG00000016893	1 retrocopy	retro_cfam_1488,
Choloepus hoffmanni	ENSCHOG00000013760	1 retrocopy	retro_chof_1372,
Callithrix jacchus	ENSCJAG00000007322	2 retrocopies	retro_cjac_1175 , retro_cjac_1922,
Echinops telfairi	ENSETEG00000000758	1 retrocopy	retro_etel_709,
Felis catus	ENSFCAG00000008944	2 retrocopies	retro_fcat_1291, retro_fcat_574,
Homo sapiens	ENSG00000159210	1 retrocopy	retro_hsap_2394,
Gorilla gorilla	ENSGGOG00000025290	1 retrocopy	retro_ggor_1816,
Macropus eugenii	ENSMEUG00000016638	1 retrocopy	retro_meug_663,
Mustela putorius furo	ENSMPUG00000015356	1 retrocopy	retro_mputfur_1425,
Mus musculus	ENSMUSG00000006058	1 retrocopy	retro_mmus_1050,
Nomascus leucogenys	ENSNLEG00000002743	1 retrocopy	retro_nleu_2520,
Oryctolagus cuniculus	ENSOCUG00000009156	2 retrocopies	retro_ocun_814, retro_ocun_996,
Pongo abelii	ENSPPYG00000008911	1 retrocopy	retro_pabe_2161,
Tarsius syrichta	ENSTSYG00000004576	1 retrocopy	retro_tsyr_843,