RetrogeneDB ID: retro_cjac_1392

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:36841639..36842114(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMED2
• Ensembl ID: ENSCJAG00000020466
• Aliases: None
• Description: None

Sequence

>retro_cjac_1392
GTCAGCTCAGGCACCAAGATGGGCCTCCTCTTAGAAGGTGGCTGAGGGTGGCTTCCTGGACATCAACGTGGAGATGACAG
GACCTGATAATAAGGGGATTTATAAAGGAGACCAAGAATCCAGTGGGAAATACACATTTGCTGCTCCCATAGATGGAACA
CATAAATTTTATTTTAGTAAGTGAGTGTCCACCATGACTCCAAAGATAGTGATATTCACCACTGCTTTTGGGGAGGCTCC
AAAAGGATAAGACGTGGAAACAGAAGCTCACTAGGACGAGCTAGTAGAAATGATCAATGAGCTGGCTGTGGCCTTGACAG
CTGTACGGCATGGAGAGGAATATGCAAAAGTCTGGGAGAGGATGCGCAGAGCCCACTGACAACACAAACACCCAGTGGTC
CTTTGGTCCTTCTTTGAAGCTCTTGTTCTAATTACCATGACATTGGGACATATCGACTACCTGAAGAGACATTTT

Alignment

ORF - retro_cjac_1392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.94 %
• Parental protein coverage: 79.21 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTSGTKMGLIFE-VAEGGFLDIDVEITGPDNKGIYKGDRESSGKYTFAAHMDGIYKFCFSNRMSTMTPKI
          V.SGTKMGL..E.VAEGGFLDI.VE.TGPDNKGIYKGD.ESSGKYTFAA..DG..KF.FS...STMTPKI
Retrocopy VSSGTKMGLLLE>VAEGGFLDINVEMTGPDNKGIYKGDQESSGKYTFAAPIDGTHKFYFSK*VSTMTPKI

Parental  VMFTIDLGEAPKGQDMETEGHQNKLKKMINVELAVAMTAVKHEQEYMEVRERIHRAINDNTNSRVVLWSF
          V.FT...GEAPKG.D.ETE.H...L..MIN.ELAVA.TAV.H..EY..V.ER..RA........VVLWSF
Retrocopy VIFTTAFGEAPKG*DVETEAH*DELVEMIN-ELAVALTAVRHGEEYAKVWERMRRAH*QHKHP-VVLWSF

Parental  FEALVLVAMTLGQIYYLKRFF
          FEALVL..MTLG.I.YLKR.F
Retrocopy FEALVLITMTLGHIDYLKRHF

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	0.09 RPM	115.18 RPM
SRP051959_heart	0.07 RPM	78.33 RPM
SRP051959_kidney	0.40 RPM	110.78 RPM
SRP051959_liver	0.24 RPM	193.93 RPM
SRP051959_lung	0.39 RPM	74.93 RPM
SRP051959_lymph_node	0.34 RPM	73.08 RPM
SRP051959_skeletal_muscle	0.09 RPM	106.88 RPM
SRP051959_spleen	0.32 RPM	103.53 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1392 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1392 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1392 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2793
Gorilla gorilla	retro_ggor_1943
Pongo abelii	retro_pabe_2227
Macaca mulatta	retro_mmul_1439

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015262	2 retrocopies	retro_amel_1923, retro_amel_337,
Bos taurus	ENSBTAG00000039630	2 retrocopies	retro_btau_52, retro_btau_819,
Choloepus hoffmanni	ENSCHOG00000012728	6 retrocopies	retro_chof_104, retro_chof_1277, retro_chof_2323, retro_chof_2601, retro_chof_2709, retro_chof_981,
Callithrix jacchus	ENSCJAG00000020466	1 retrocopy	retro_cjac_1392 ,
Echinops telfairi	ENSETEG00000000556	2 retrocopies	retro_etel_2109, retro_etel_2154,
Homo sapiens	ENSG00000086598	1 retrocopy	retro_hsap_2793,
Gorilla gorilla	ENSGGOG00000028536	1 retrocopy	retro_ggor_1943,
Macaca mulatta	ENSMMUG00000031491	2 retrocopies	retro_mmul_1439, retro_mmul_613,
Mustela putorius furo	ENSMPUG00000001598	1 retrocopy	retro_mputfur_1241,
Mus musculus	ENSMUSG00000029390	2 retrocopies	retro_mmus_1361, retro_mmus_3262,
Nomascus leucogenys	ENSNLEG00000001652	2 retrocopies	retro_nleu_2454, retro_nleu_2794,
Otolemur garnettii	ENSOGAG00000009192	1 retrocopy	retro_ogar_2548,
Pongo abelii	ENSPPYG00000005090	3 retrocopies	retro_pabe_1919, retro_pabe_2227, retro_pabe_3597,