RetrogeneDB ID: retro_cjac_4017

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL288498.1:11363..12180(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020803
• Aliases: None
• Description: None

Sequence

>retro_cjac_4017
GTGACCAAGAAGCTCTTGCAGATGGACCTGAACACCCTTCTAGGCATCCAGGAGATAGCGACAGACAAAGAGGTGAAGAA
GGCCTACAGGCAGAAGGCCCTCTCCTGCCACCCAGACAAAAATCCCGATAATCCCAGAGCCGCTGAATTCTTCCACCAGC
TTTCCCGGACCTTAGAGGTACTGACCGATGCTGCAGCCAGGGCTGCATGACAAGGTCAGGAAAGCCGGGAAGCAGGCAGC
AGAGAGGACCCAGAAACTTGAAGACAGACGGAAGAGAATGAGGCTTGAACTGGGGGCTCAGGAGTGGCAGGCCCAGGCTC
TGGGGAGCGAGGAAGCCCAGGGCAGCTGGAGACCCAAGACGCTGGAGCAAGAGATCAGGTGCCTTCAAGAAGAGGGCACG
TAGCAGCTGGAGGAACAGCAGAGGCCGATCCGGGAGCAGATCCTCCAAGAACATGACCAGAGGTGGAGAGAAAAGGCCGA
AAGCACTGAAGGCAGAGGAAGCCCCAAACTGAAGCTCAAATGGAAGTGTAAGATGGAGGATGCCTCAAAAGGCAGCTACT
CCCAAGGTGTCCTCCTGCAGAAGTACAGGGAGGTTCACAACCTGGTGCTTTCCAGCAAGAAAGCAGGAATAGCCGTGGTG
GAGTTTGCCACAGTCAAGGCTGCGGAGCTGGCTGTCCAGAATGAAGTTGGCTTGGTTGAGAACCCGCTGAAGATTTACTG
ATTGGAGGGACGGCCCCAGGGCACAGTGCACCCCAGCCACCCAGGGCAGTCCAAGGACTCAGCGCTGCTGGACAGGGACT
CTGAGAGCCTTGTCATC

Alignment

ORF - retro_cjac_4017 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.84 %
• Parental protein coverage: 90.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VTKELLQMDLYALLGIEEKAADKEVKKAFRQKALSCHPDKNPDNPRAAELFHQLSQALEVLTDAAARAA-
          VTK.LLQMDL..LLGI.E.A.DKEVKKA.RQKALSCHPDKNPDNPRAAE.FHQLS..LEVLTD.AA..A.
Retrocopy VTKKLLQMDLNTLLGIQEIATDKEVKKAYRQKALSCHPDKNPDNPRAAEFFHQLSRTLEVLTD-AAARA>

Parental  YDKVRKAKKQAAERTQKLDEKRKKVKLDLEARERQAQAQESEEEEESRSTRTLEQEIERLREEGSRQLEE
          .DKVRKA.KQAAERTQKL...RK...L.L.A.E.QAQA..SEE...S....TLEQEI..L.EEG..QLEE
Retrocopy HDKVRKAGKQAAERTQKLEDRRKRMRLELGAQEWQAQALGSEEAQGSWRPKTLEQEIRCLQEEGT*QLEE

Parental  QQRLIREQIRQDHDQRLRGKTENTEGQGTPKLKLKWKCKKEDESKGGYSKDVLLQLLQKYGEVLNLVLSS
          QQR.IREQI.Q.HDQR.R.K.E.TEG.G.PKLKLKWKCK.ED.SKG.YS..VLLQ...KY.EV.NLVLSS
Retrocopy QQRPIREQILQEHDQRWREKAESTEGRGSPKLKLKWKCKMEDASKGSYSQGVLLQ---KYREVHNLVLSS

Parental  KKAGTAVVEFATVRAAELAVQNEVGLVDNPLKISWLEGQPQDAMGRSHPGLSKGSVVSERDYESLVM
          KKAG.AVVEFATV.AAELAVQNEVGLV.NPLKI..LEG.PQ.....SHPG.SK.S....RD.ESLV.
Retrocopy KKAGIAVVEFATVKAAELAVQNEVGLVENPLKIY*LEGRPQGTVHPSHPGQSKDSALLDRDSESLVI

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	3.02 RPM
SRP051959_heart	0.00 RPM	3.47 RPM
SRP051959_kidney	0.00 RPM	5.15 RPM
SRP051959_liver	0.00 RPM	2.53 RPM
SRP051959_lung	0.00 RPM	5.84 RPM
SRP051959_lymph_node	0.00 RPM	5.91 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.06 RPM
SRP051959_spleen	0.00 RPM	5.61 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4017 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4017 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4017 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020803	4 retrocopies	retro_cjac_1013, retro_cjac_4017 , retro_cjac_738, retro_cjac_820,
Cavia porcellus	ENSCPOG00000014110	1 retrocopy	retro_cpor_693,
Homo sapiens	ENSG00000104129	2 retrocopies	retro_hsap_2363, retro_hsap_3468,
Gorilla gorilla	ENSGGOG00000000051	1 retrocopy	retro_ggor_2340,
Macropus eugenii	ENSMEUG00000005641	2 retrocopies	retro_meug_1387, retro_meug_2001,
Myotis lucifugus	ENSMLUG00000014835	1 retrocopy	retro_mluc_317,
Macaca mulatta	ENSMMUG00000013160	1 retrocopy	retro_mmul_1574,
Mus musculus	ENSMUSG00000034278	1 retrocopy	retro_mmus_3346,
Nomascus leucogenys	ENSNLEG00000003257	1 retrocopy	retro_nleu_343,
Pongo abelii	ENSPPYG00000006360	1 retrocopy	retro_pabe_2864,
Pan troglodytes	ENSPTRG00000006929	2 retrocopies	retro_ptro_1729, retro_ptro_2351,
Rattus norvegicus	ENSRNOG00000012368	2 retrocopies	retro_rnor_18, retro_rnor_2319,