RetrogeneDB ID: retro_cjac_1922

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:71128821..71129594(-)
• Located in intron of: None

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_1922
ATGCACCGCTGCGGGGTGGGAGCTGACACCATTGCCAAGAAAACAACTTGCAGAGGCCAAGTATAAGGAGCGAGGGATGG
TCCTGGCTGAGAACCAGCTAGCCCAGTTGTCAAAGCAGTTGGACATGTTCAAGACCAACCTGGAGGAATTTGCCAGCAAG
CACAAGCAGGAGATCCGGAAGAATTATGAGTTCCGTATGCAGTTCCAGGACATGTGTGCAACCATTGCCATGGATCCTTT
GGCCTCTGGAAAAGGATTTTGGTCTGAGATGCTGGACATGGGGGACTTTTATGAACTAGATGTCCAAATTTATTGAAGTG
TGCCTGGTGCTGAAGCATCAGAAGGGAGGTCTGATAACTCTGGAGGAACTACATCAACAGGTGTTGAAGGGAAGGGGCAA
GTTCACCCAGGATGTCAGTCAAGACGACCTGATCAGGGCCATCAGGAAACTAAAGGCACTTGGGACTGGCTTAGGCATCA
TCCCTGTAGGTGGCACTTACCTCATTCAGTCTGTTCCAGCTGAGCTCAATATGGATCACACCGTGGTGCTGCATCTGCCA
GAGAAAAATGGCTACATGACTGTCAGTAAGATCAAAGCCAGTCTTAAATGGCAGACCGAGTGAGTGCGGCAAGTCCTGCA
ACACCTGCTGAAGGAAAGGCTGGTGTGGCTGGACTTGCAGGCCCCAGGGGAGGCCCACTACCGGCTGCCAGGTCTCTTCA
CTGACCTCTGCTCCCGGGAGATTACAGCTGAGGAGGCCGGAGAAGCCTTCCCC

Alignment

ORF - retro_cjac_1922 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.85 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MHRRGVGAGAIAKK-KLAEAKYKERGTVLAEDQLAQMSKQLDMFKTNLEEFASKHKQEIRKNPEFRVQFQ
          MHR.GVGA..IAKK..LAEAKYKERG.VLAE.QLAQ.SKQLDMFKTNLEEFASKHKQEIRKN.EFR.QFQ
Retrocopy MHRCGVGADTIAKK>QLAEAKYKERGMVLAENQLAQLSKQLDMFKTNLEEFASKHKQEIRKNYEFRMQFQ

Parental  DMCATIGVDPLASFSLFFKKMFNF--YYELGVQI-IEVCLALKHRNGEQKITSHTHCKLFSGRGPCLFTD
          DMCATI..DPLAS...F...M......YEL.VQI.IEVCL.LKH..G........H.....GRG.....D
Retrocopy DMCATIAMDPLASGKGFWSEMLDMGDFYELDVQI>IEVCLVLKHQKGGLITLEELHQQVLKGRGK-FTQD

Parental  VVEDDLIRAIKKLKALGTGFCIIPVGGTYLIQSVPAELNMDHTVVLQLAEKNGYVTVSEIKASLKWETER
          V..DDLIRAI.KLKALGTG..IIPVGGTYLIQSVPAELNMDHTVVL.L.EKNGY.TVS.IKASLKW.TE.
Retrocopy VSQDDLIRAIRKLKALGTGLGIIPVGGTYLIQSVPAELNMDHTVVLHLPEKNGYMTVSKIKASLKWQTE*

Parental  ARQVLEHLLKEGLAWLDLQAPGEAHYWLPALFTDLYSQEITAEEAREALP
          .RQVL.HLLKE.L.WLDLQAPGEAHY.LP.LFTDL.S.EITAEEA.EA.P
Retrocopy VRQVLQHLLKERLVWLDLQAPGEAHYRLPGLFTDLCSREITAEEAGEAFP

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	0.35 RPM	7.57 RPM
SRP051959_heart	0.30 RPM	7.24 RPM
SRP051959_kidney	0.27 RPM	9.70 RPM
SRP051959_liver	0.22 RPM	7.06 RPM
SRP051959_lung	0.23 RPM	8.30 RPM
SRP051959_lymph_node	0.30 RPM	9.73 RPM
SRP051959_skeletal_muscle	0.26 RPM	7.34 RPM
SRP051959_spleen	0.23 RPM	8.68 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1922 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1922 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1922 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,