RetrogeneDB ID: retro_cjac_1133

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:37750913..37751370(-)
• Located in intron of: ENSCJAG00000006481

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYB
• Ensembl ID: ENSCJAG00000014610
• Aliases: None
• Description: nuclear transcription factor Y, beta [Source:HGNC Symbol;Acc:7805]

Sequence

>retro_cjac_1133
CTGGAGGTGCATGGAGACCACTGCATGACACGGGCTTCTGCGCTGGGAACTTCTGAAGACTGCACTGGAGGAGTCATTAC
ATTACACAGCCTCATGGTGACAGTGAGGACAGCATGAACGGTCATGAAGGTACAAATGGTTCAAAAGAAAGTTGCAGAGA
ATAAGATATACATTGTTTTACTGCACGTATCGCAAGGATAATGAAACATGCCATGTCTCAAATGGGAAATACCCAAGAAA
GTGTTCGAGAATGTGTATGTGCGTTCATCAGCTTTCTAACATCCGAGGCAAGTGACCGAGACTAAGAGAATCGGAAGTGA
CCAGTGGAGAGGATCTTCTTGCTGTGTCTACAGTAGGCTTCGACAGTTATGTGGGACCTCCGAAACTATCCCTTCAGAAA
CTCAGAGAGGCTAGGAAAGGAGAGAAGGGAATTGGTGGAGAAGTCAGGGCTACAGAG

Alignment

ORF - retro_cjac_1133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.63 %
• Parental protein coverage: 76.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTMDGDSSTTDASQLGISADYIGG-SHYVIQPHDDTEDSMNDHEDTNGSKESFREQDIYLPIANVARIMK
          ....GD...T.AS.LG.S.D..GG.SHY..QPH.D.EDSMN.HE.TNGSKES.RE.DI....A..ARIMK
Retrocopy LEVHGDHCMTRASALGTSEDCTGG<SHYITQPHGDSEDSMNGHEGTNGSKESCRE*DIHCFTARIARIMK

Parental  NAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRK-TINGEDILFAMSTLGFDSYVEPLKLYL
          .A..Q.G.......E.V.ECV..FISF.TSEAS.R...E.RK....GED.L.A.ST.GFDSYV.P.KL.L
Retrocopy HAMSQMG----NTQESVRECVCAFISFLTSEASDR-D*ENRK<VTSGEDLL-AVSTVGFDSYVGPPKLSL

Parental  QKFREAMKGEKGIGGAVTATD
          QK.REA.KGEKGIGG.V.AT.
Retrocopy QKLREARKGEKGIGGEVRATE

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	0.20 RPM	20.26 RPM
SRP051959_heart	0.02 RPM	26.45 RPM
SRP051959_kidney	0.31 RPM	30.11 RPM
SRP051959_liver	1.34 RPM	23.18 RPM
SRP051959_lung	0.00 RPM	27.12 RPM
SRP051959_lymph_node	0.00 RPM	29.75 RPM
SRP051959_skeletal_muscle	0.00 RPM	21.05 RPM
SRP051959_spleen	0.00 RPM	24.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1133 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1133 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1133 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006686	1 retrocopy	retro_amel_940,
Bos taurus	ENSBTAG00000030744	1 retrocopy	retro_btau_1681,
Canis familiaris	ENSCAFG00000029177	1 retrocopy	retro_cfam_1677,
Callithrix jacchus	ENSCJAG00000014610	1 retrocopy	retro_cjac_1133 ,
Callithrix jacchus	ENSCJAG00000017917	1 retrocopy	retro_cjac_4121,
Cavia porcellus	ENSCPOG00000003213	1 retrocopy	retro_cpor_901,
Dasypus novemcinctus	ENSDNOG00000009984	3 retrocopies	retro_dnov_1536, retro_dnov_758, retro_dnov_855,
Felis catus	ENSFCAG00000026471	1 retrocopy	retro_fcat_207,
Homo sapiens	ENSG00000120837	2 retrocopies	retro_hsap_2827, retro_hsap_4047,
Gorilla gorilla	ENSGGOG00000008866	1 retrocopy	retro_ggor_2714,
Myotis lucifugus	ENSMLUG00000005468	1 retrocopy	retro_mluc_1764,
Macaca mulatta	ENSMMUG00000022570	3 retrocopies	retro_mmul_1433, retro_mmul_2119, retro_mmul_2335,
Mustela putorius furo	ENSMPUG00000012064	3 retrocopies	retro_mputfur_1531, retro_mputfur_1563, retro_mputfur_1567,
Nomascus leucogenys	ENSNLEG00000006543	2 retrocopies	retro_nleu_1203, retro_nleu_2061,
Oryctolagus cuniculus	ENSOCUG00000004415	4 retrocopies	retro_ocun_1334, retro_ocun_1816, retro_ocun_1824, retro_ocun_1845,
Ochotona princeps	ENSOPRG00000008117	2 retrocopies	retro_opri_36, retro_opri_657,
Pongo abelii	ENSPPYG00000004892	3 retrocopies	retro_pabe_2201, retro_pabe_2803, retro_pabe_3319,
Ictidomys tridecemlineatus	ENSSTOG00000005279	1 retrocopy	retro_itri_1851,
Tupaia belangeri	ENSTBEG00000005731	1 retrocopy	retro_tbel_4360,