RetrogeneDB ID: retro_cjac_534

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 1:67060769..67061374(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L1
• Ensembl ID: ENSCJAG00000001115
• Aliases: None
• Description: nucleosome assembly protein 1-like 1 [Source:HGNC Symbol;Acc:7637]

Sequence

>retro_cjac_534
CCTATTCTGAAGCACTTGAAAGATATTAAAGTGAAGTTCTCAGATGCTGGCCAGCCTATGAGTTTTCTCTTAGAATTTCT
CTTTGAGCCCAATGAGTATTTTACGAATGAAGTGCTGACAAAGACATATACAATGAAGTTAGAACCAGATGATTCTGATC
CCTTTTCTTTTGATGGACCAGAAGTTACGGGTTGTACAGGGTGCCAGATAGATAGGGAAGAAGGAAAGAATGTGACTTTG
CAAACCAGTAAGAAGCAGCAGAAACAAAAGGGATATGGGATAGTTTGTACTGTGACTAAAACAGTTTCTAATGACTCTTT
CTTTAATTTTGTTCCCCTCCTGAAGTTCCTGAGAGTGGAGATCTGGTTGATGCTGCTGAAGCTATCCTTACTGCAGACTT
CAAAATTGGTCACTTTTTACATGAGTATATAATCCCAAGATCAGTGTTATAATTTACTGGAGAAGCTATTGAAGATGATG
ATGATGATGATGATGATGATGAAGGTGAAGAAGCATATGAGGAAGGGGAAGAAGAAGGAGATAAGAAAAATGATCCAGAC
TATGACCCGAAGAAGGATCAAAACCCAGCAGAGTGCAAGCAGCAG

Alignment

ORF - retro_cjac_534 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.35 %
• Parental protein coverage: 57.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PILKHLKDIKVKFSDAGQPMSFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQI
          PILKHLKDIKVKFSDAGQPMSF.LEF.FEPNEYFTNEVLTKTY.M..EPDDSDPFSFDGPE..GCTGCQI
Retrocopy PILKHLKDIKVKFSDAGQPMSFLLEFLFEPNEYFTNEVLTKTYTMKLEPDDSDPFSFDGPEVTGCTGCQI

Parental  DWKKGKNVTLKTIKKKQKHKGRGTVRTVTKTVSNDSFFNFF-APPEVPESGDLDDDAEAILAADFEIGHF
          D...GKNVTL.T.KK.QK.KG.G.V.TVTKTVSNDSFFNF...PPEVPESGDL.D.AEAIL.ADF.IGHF
Retrocopy DREEGKNVTLQTSKKQQKQKGYGIVCTVTKTVSNDSFFNFV<SPPEVPESGDLVDAAEAILTADFKIGHF

Parental  LRERIIPRSVLYFTGEAIEDDDDDYDEEGEEADEEGEEE-GDEENDPDYDPKKDQNPAECKQQ
          L.E.IIPRSVL.FTGEA.............E...E..EE.GD..NDPDYDPKKDQNPAECKQQ
Retrocopy LHEYIIPRSVL*FTGEAXXXXXXXXXXXXGEEAYEEGEEEGDKKNDPDYDPKKDQNPAECKQQ

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	47.39 RPM
SRP051959_heart	0.02 RPM	82.67 RPM
SRP051959_kidney	0.00 RPM	72.39 RPM
SRP051959_liver	0.02 RPM	34.33 RPM
SRP051959_lung	0.02 RPM	107.41 RPM
SRP051959_lymph_node	0.02 RPM	104.52 RPM
SRP051959_skeletal_muscle	0.00 RPM	80.98 RPM
SRP051959_spleen	0.00 RPM	92.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_534 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_534 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_534 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 19 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Choloepus hoffmanni	ENSCHOG00000003210	2 retrocopies	retro_chof_1095, retro_chof_2057,
Callithrix jacchus	ENSCJAG00000001115	1 retrocopy	retro_cjac_534 ,
Felis catus	ENSFCAG00000000279	1 retrocopy	retro_fcat_1037,
Homo sapiens	ENSG00000187109	3 retrocopies	retro_hsap_1199, retro_hsap_2696, retro_hsap_833,
Gorilla gorilla	ENSGGOG00000003883	3 retrocopies	retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Nomascus leucogenys	ENSNLEG00000004682	4 retrocopies	retro_nleu_1192, retro_nleu_2085, retro_nleu_265, retro_nleu_2766,
Otolemur garnettii	ENSOGAG00000010319	4 retrocopies	retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666,
Pongo abelii	ENSPPYG00000004786	2 retrocopies	retro_pabe_2287, retro_pabe_999,
Pan troglodytes	ENSPTRG00000005240	4 retrocopies	retro_ptro_1820, retro_ptro_582, retro_ptro_694, retro_ptro_819,
Pteropus vampyrus	ENSPVAG00000016032	2 retrocopies	retro_pvam_1282, retro_pvam_306,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,
Ictidomys tridecemlineatus	ENSSTOG00000003046	2 retrocopies	retro_itri_1007, retro_itri_416,
Vicugna pacos	ENSVPAG00000007290	3 retrocopies	retro_vpac_435, retro_vpac_441, retro_vpac_601,