RetrogeneDB ID: retro_cjac_3268

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:16268313..16268795(-)
• Located in intron of: ENSCJAG00000002622

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000003731
• Aliases: None
• Description: None

Sequence

>retro_cjac_3268
GCTGCTTTTCTAACCCAAACTGTGTGTCTTGATGACACTACAGTATAGGTTGAAAGATGGGATATAGCTCGTCAAGAACA
ATACCGTAGCCTAGCACCGATGTACTACAGAGGACACAAGCAGCCATAGTTGTATATGATAACACAAATGAGGAGTCCTC
TGCAAGAGCAAAAAATTGGGTTAAAGAACTTCAGAGGCAAGCAAGTTCTAACATGGTAGTAGTTTTATCAGGAAACAAGG
CTGACCTCGCAAAGGAAAGAGTAGTAGATTTCCAGGAAGCACAGTCCTATGCAGATGACAATAGTTTATTATTCATGAAG
ACAGCAGCTGAAACATCAATGAATGCAAATGAGATATTCATGGCAATAGCTAAAAAATTGCCAAAGAAGGAACCACCAAA
TCCAGGAGCAAATTCTGCCAGACGAAGAGGAGTAAACCTTGCTGAACTTACACAACCAAGCAGGAGTCAGTGTTGCAGTA
AC

Alignment

ORF - retro_cjac_3268 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.1 %
• Parental protein coverage: 74.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAFLTQTVCLDDTTVKFEIWDTAGQERYHSLAPMYYRG-AQAAIVVYDITNEESFARAKNWVKELQRQAS
          AAFLTQTVCLDDTTV..E.WD.A.QE.Y.SLAPMYYRG..QAAIVVYD.TNEES.ARAKNWVKELQRQAS
Retrocopy AAFLTQTVCLDDTTV*VERWDIARQEQYRSLAPMYYRG<TQAAIVVYDNTNEESSARAKNWVKELQRQAS

Parental  PNIVIALSGNKADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKNEPQNPGANS
          .N.V..LSGNKADLA..R.VDFQEAQSYADDNSLLFM.T.A.TSMN.NEIFMAIAKKLPK.EP.NPGANS
Retrocopy SNMVVVLSGNKADLAKERVVDFQEAQSYADDNSLLFMKTAAETSMNANEIFMAIAKKLPKKEPPNPGANS

Parental  ARGRGVDLTEPTQPTRSQCCSN
          AR.RGV.L.E.TQP.RSQCCSN
Retrocopy ARRRGVNLAELTQPSRSQCCSN

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	0.33 RPM	27.65 RPM
SRP051959_heart	0.14 RPM	23.56 RPM
SRP051959_kidney	0.22 RPM	20.26 RPM
SRP051959_liver	0.15 RPM	19.58 RPM
SRP051959_lung	0.34 RPM	36.33 RPM
SRP051959_lymph_node	0.25 RPM	22.92 RPM
SRP051959_skeletal_muscle	0.07 RPM	17.23 RPM
SRP051959_spleen	0.46 RPM	26.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3268 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3268 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3268 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1074
Gorilla gorilla	retro_ggor_848
Pongo abelii	retro_pabe_894
Macaca mulatta	retro_mmul_839

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Parental genes homology:

Parental genes homology involve 23 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000954	1 retrocopy	retro_amel_958,
Bos taurus	ENSBTAG00000046385	1 retrocopy	retro_btau_300,
Callithrix jacchus	ENSCJAG00000000472	2 retrocopies	retro_cjac_189, retro_cjac_1948,
Callithrix jacchus	ENSCJAG00000003731	1 retrocopy	retro_cjac_3268 ,
Callithrix jacchus	ENSCJAG00000004529	2 retrocopies	retro_cjac_1178, retro_cjac_1179,
Callithrix jacchus	ENSCJAG00000007527	2 retrocopies	retro_cjac_1215, retro_cjac_1879,
Callithrix jacchus	ENSCJAG00000019039	2 retrocopies	retro_cjac_1715, retro_cjac_842,
Cavia porcellus	ENSCPOG00000005322	2 retrocopies	retro_cpor_1213, retro_cpor_219,
Dipodomys ordii	ENSDORG00000012429	1 retrocopy	retro_dord_288,
Felis catus	ENSFCAG00000004455	2 retrocopies	retro_fcat_1349, retro_fcat_984,
Homo sapiens	ENSG00000144566	1 retrocopy	retro_hsap_1074,
Gorilla gorilla	ENSGGOG00000015981	1 retrocopy	retro_ggor_848,
Loxodonta africana	ENSLAFG00000008321	1 retrocopy	retro_lafr_267,
Macaca mulatta	ENSMMUG00000006992	2 retrocopies	retro_mmul_227, retro_mmul_839,
Monodelphis domestica	ENSMODG00000014793	2 retrocopies	retro_mdom_1219, retro_mdom_1993,
Mus musculus	ENSMUSG00000017831	1 retrocopy	retro_mmus_1645,
Nomascus leucogenys	ENSNLEG00000003434	1 retrocopy	retro_nleu_2466,
Oryctolagus cuniculus	ENSOCUG00000012200	1 retrocopy	retro_ocun_1034,
Pongo abelii	ENSPPYG00000014074	2 retrocopies	retro_pabe_3094, retro_pabe_894,
Pan troglodytes	ENSPTRG00000014682	1 retrocopy	retro_ptro_731,
Ictidomys tridecemlineatus	ENSSTOG00000026229	1 retrocopy	retro_itri_398,
Tarsius syrichta	ENSTSYG00000007642	3 retrocopies	retro_tsyr_1544, retro_tsyr_315, retro_tsyr_946,
Tursiops truncatus	ENSTTRG00000001374	1 retrocopy	retro_ttru_949,