RetrogeneDB ID: retro_cjac_1641

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:35000480..35000812(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFN1
• Ensembl ID: ENSCJAG00000011719
• Aliases: LOC100395089, PFN1, profilin-1
• Description: profilin 1 [Source:HGNC Symbol;Acc:8881]

Sequence

>retro_cjac_1641
GCCCTCTGGGCCGCAGTCCCCAAGAAAACCTTCGTCAACATCACGCCAGCCGAGACTGCTGTCCTGGTTGGCAAAGACCA
GTCAAGTTTTTCGTGAATGGGCTGACACTCGGGGGCCAGAAACGTTCGGTGATCCGGGACTGACTGCTGCAGGATGGGGA
ATTTAGCAAGGGTCTTCACACCAAGAGCACAGGTGGAGCCCCCACCTTCAGTGTCACTGTCACCAAGACCGACAAGACGC
CAGTCCTGCTGATGGGCAAAGAAGGTGTCCACGGTGGTTCGATCAACAAGAAATGTTATGAAATGGCCTCCCACCTTCGG
TGTTCCCAGTAC

Alignment

ORF - retro_cjac_1641 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.93 %
• Parental protein coverage: 79.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SVWAAVPGKTFVNITPAEVGVLVGKDRSSF-YVNGLTLGGQKCSVIRDSLLQDGEFSMDLRTKSTGGAPT
          ..WAAVP.KTFVNITPAE..VLVGKD.SSF..VNGLTLGGQK.SVIRD.LLQDGEFS..L.TKSTGGAPT
Retrocopy ALWAAVPKKTFVNITPAETAVLVGKDQSSF<FVNGLTLGGQKRSVIRD*LLQDGEFSKGLHTKSTGGAPT

Parental  FNVTVTKTDKTLVLLMGKEGVHGGLINKKCYEMASHLRRAQY
          F.VTVTKTDKT.VLLMGKEGVHGG.INKKCYEMASHLR..QY
Retrocopy FSVTVTKTDKTPVLLMGKEGVHGGSINKKCYEMASHLRCSQY

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	86.64 RPM
SRP051959_heart	0.00 RPM	34.89 RPM
SRP051959_kidney	0.00 RPM	48.59 RPM
SRP051959_liver	0.00 RPM	49.21 RPM
SRP051959_lung	0.00 RPM	76.42 RPM
SRP051959_lymph_node	0.00 RPM	129.77 RPM
SRP051959_skeletal_muscle	0.02 RPM	34.53 RPM
SRP051959_spleen	0.00 RPM	83.13 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1641 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1641 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1641 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_574

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006193	2 retrocopies	retro_amel_1712, retro_amel_1781,
Bos taurus	ENSBTAG00000004915	1 retrocopy	retro_btau_141,
Callithrix jacchus	ENSCJAG00000001271	1 retrocopy	retro_cjac_4029,
Callithrix jacchus	ENSCJAG00000011719	2 retrocopies	retro_cjac_1023, retro_cjac_1641 ,
Cavia porcellus	ENSCPOG00000013136	1 retrocopy	retro_cpor_1216,
Equus caballus	ENSECAG00000021116	3 retrocopies	retro_ecab_171, retro_ecab_28, retro_ecab_559,
Homo sapiens	ENSG00000108518	10 retrocopies	retro_hsap_214, retro_hsap_215, retro_hsap_221, retro_hsap_223, retro_hsap_224, retro_hsap_352, retro_hsap_446, retro_hsap_447, retro_hsap_450, retro_hsap_451,
Gorilla gorilla	ENSGGOG00000022394	3 retrocopies	retro_ggor_285, retro_ggor_289, retro_ggor_366,
Macaca mulatta	ENSMMUG00000002772	5 retrocopies	retro_mmul_407, retro_mmul_527, retro_mmul_528, retro_mmul_574, retro_mmul_732,
Mus musculus	ENSMUSG00000018293	1 retrocopy	retro_mmus_1326,
Nomascus leucogenys	ENSNLEG00000017446	6 retrocopies	retro_nleu_16, retro_nleu_1870, retro_nleu_2425, retro_nleu_2429, retro_nleu_848, retro_nleu_886,
Otolemur garnettii	ENSOGAG00000031395	3 retrocopies	retro_ogar_1680, retro_ogar_2143, retro_ogar_3351,
Procavia capensis	ENSPCAG00000000291	1 retrocopy	retro_pcap_27,
Pelodiscus sinensis	ENSPSIG00000004124	1 retrocopy	retro_psin_8,
Pan troglodytes	ENSPTRG00000008616	5 retrocopies	retro_ptro_185, retro_ptro_196, retro_ptro_276, retro_ptro_332, retro_ptro_333,
Rattus norvegicus	ENSRNOG00000003975	1 retrocopy	retro_rnor_1623,
Sus scrofa	ENSSSCG00000017905	1 retrocopy	retro_sscr_275,
Ictidomys tridecemlineatus	ENSSTOG00000028950	1 retrocopy	retro_itri_129,
Tursiops truncatus	ENSTTRG00000001299	1 retrocopy	retro_ttru_14,
Vicugna pacos	ENSVPAG00000005327	3 retrocopies	retro_vpac_389, retro_vpac_395, retro_vpac_457,