RetrogeneDB ID: retro_cjac_2027

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:27282259..27282648(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOC
• Ensembl ID: ENSCJAG00000013657
• Aliases: None
• Description: None

Sequence

>retro_cjac_2027
CAAGAAGGCTATGATCAACTGTGGCCTCTCTCCCACCCCGACACTGATGCCATCCTCATGTGCTTCTCCATCCACAGCCT
CGACAGCCTGGAAAACATTCCTGAGAAGTGGACCCCAGAGGTGAAGCCCTTCTGCCCCAACGTGCCGGTCATCCTAGTGG
GGAATAAGGACGTGAGGCAAGATGATCACACCAGGAGAGAGCTGGCCAAGACGAAGCAGGAGCCCGTTCAGTCTGAGGAA
GGCCGAGACACGGCGAATCGGATCAGTGCCTTTGGCTGACTTGAGTGCTCAGCCAAGACCAAGGAGGGAGTGCGGGAGGT
GTTTGAGACGGCCACTGGGGCTGGCCTCCAGGTCTGCAAGAACAAGCACGGGAGGGGTGTCCCATTCTC

Alignment

ORF - retro_cjac_2027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 67.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRQDEHTRRELA
          QE.YD.L.PLS.PDTD.ILMCFSI.S.DSLENIPEKWTPEVK.FCPNVP.ILVGNK.D.RQD.HTRRELA
Retrocopy QEGYDQLWPLSHPDTDAILMCFSIHSLDSLENIPEKWTPEVKPFCPNVPVILVGNK-DVRQDDHTRRELA

Parental  KMKQEPVRSEEGRDMANRISAFGYLECSAKTKEGVREVFEMATRAGLQVRKNKR-RRGCPIL
          K.KQEPV.SEEGRD.ANRISAFG.LECSAKTKEGVREVFE.AT.AGLQV.KNK..R.GCPIL
Retrocopy KTKQEPVQSEEGRDTANRISAFG*LECSAKTKEGVREVFETATGAGLQVCKNKH<REGCPIL

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	17.62 RPM
SRP051959_heart	0.00 RPM	16.72 RPM
SRP051959_kidney	0.00 RPM	21.08 RPM
SRP051959_liver	0.00 RPM	20.51 RPM
SRP051959_lung	0.00 RPM	17.57 RPM
SRP051959_lymph_node	0.00 RPM	6.16 RPM
SRP051959_skeletal_muscle	0.00 RPM	15.26 RPM
SRP051959_spleen	0.00 RPM	12.63 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2027 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2027 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2027 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014299	1 retrocopy	retro_btau_1171,
Canis familiaris	ENSCAFG00000013413	1 retrocopy	retro_cfam_1152,
Callithrix jacchus	ENSCJAG00000003904	3 retrocopies	retro_cjac_1306, retro_cjac_2010, retro_cjac_411,
Callithrix jacchus	ENSCJAG00000013018	1 retrocopy	retro_cjac_3930,
Callithrix jacchus	ENSCJAG00000013657	2 retrocopies	retro_cjac_1657, retro_cjac_2027 ,
Equus caballus	ENSECAG00000010174	3 retrocopies	retro_ecab_112, retro_ecab_257, retro_ecab_932,
Ficedula albicollis	ENSFALG00000000736	1 retrocopy	retro_falb_11,
Gorilla gorilla	ENSGGOG00000002741	2 retrocopies	retro_ggor_18, retro_ggor_732,
Macropus eugenii	ENSMEUG00000004807	1 retrocopy	retro_meug_37,
Monodelphis domestica	ENSMODG00000000981	1 retrocopy	retro_mdom_1245,
Otolemur garnettii	ENSOGAG00000027678	3 retrocopies	retro_ogar_2606, retro_ogar_3360, retro_ogar_58,
Sarcophilus harrisii	ENSSHAG00000001981	1 retrocopy	retro_shar_455,
Taeniopygia guttata	ENSTGUG00000017533	1 retrocopy	retro_tgut_11,
Tetraodon nigroviridis	ENSTNIG00000015041	1 retrocopy	retro_tnig_2,
Xenopus tropicalis	ENSXETG00000006898	1 retrocopy	retro_xtro_15,
Xiphophorus maculatus	ENSXMAG00000008103	1 retrocopy	retro_xmac_13,