RetrogeneDB ID: retro_cjac_3118

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:26077102..26077722(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF3C6
• Ensembl ID: ENSCJAG00000005248
• Aliases: None
• Description: general transcription factor IIIC, polypeptide 6, alpha 35kDa [Source:HGNC Symbol;Acc:20872]

Sequence

>retro_cjac_3118
ATGGCAGCAGCAGAGGAACAGAATCCAGAGGATGGAGAAGAGGAGGGAAGAGAAAGGAAAACAGTCGGTTCTCAAGGAAT
GGTCAGAAATTACTGATTCAAACTTTCTTTCAAAATGTGAAAATAAATGCAAAATTTTGAGGATTGACATCAAGCAGCCC
TTTCTCCAAGTGGACAGATATGTCTTGGCTGGGGAGTAAGAAGACACTCTTGGGACCTGTGTTATATTTGAATAAAATGT
TGAACATGTGAATACAGAGGGCAAGATAGAACACTGCTAAAATACAAGTGCCATGCAGGGAAGAAGTCAGCATGGCAAGA
ACTCTTCTGACAGAAGAGGAGGGAGGAGAGAACAGATGGGGTGGAATGGCTGCAAATCACGGACGAAGATTTCTCCTCTA
GACCCGACATAGTTTGTAGCTTTCTATATAAAAATGAAGATGAAGAAATGGTAGCTTCAGCCTCAGATAAACCTTTGGAA
TTGGAAGAAAGATTCAAATGAAAGACAGTTCAAACCTGAGTTGTGAACAGGAGAAGCCACTGCACGTGGACATAGAGGAT
TCTGGTCCTCTTCATGACATCCCTTCTGAGACAGAAGGTTCTGTGTTTACAGAAACTCAA

Alignment

ORF - retro_cjac_3118 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 98.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAVDQRSLED--EE-EEEQEQLVLVELSGIIDSDFLSKCENKCKILGIDTERPILQVDSCVFAGEYEDT
          MAA......ED..EE.EE...Q.VL.E.S.I.DS.FLSKCENKCKIL.ID...P.LQVD..V.AGE.EDT
Retrocopy MAAAEEQNPEDGEEE>EEKGKQSVLKEWSEITDSNFLSKCENKCKILRIDIKQPFLQVDRYVLAGE*EDT

Parental  LGTCVIFEENVEHADTEGS-NKTVLKYKCHTMKKLSMTRTLLTEKKEGEENIGGVEWLQIKDNDFSYRPN
          LGTCVIFE.NVEH..TEG....T.LKYKCH..KK.......L...K..EE...GVEWLQI.D.DFS.RP.
Retrocopy LGTCVIFE*NVEHVNTEGK<DRTLLKYKCHAGKKSAWQE--LF*QKRREERTDGVEWLQITDEDFSSRPD

Parental  MICSFLHENEDEEVVASAPDKPLELEEE-EIQMKDSSNLSCEQEKPLHLEIEDSGTLIDIPSETEGSIFM
          ..CSFL..NEDEE.VASA.DKPLEL.EE..IQMKDSSNLSCEQEKPLH..IEDSG.L.DIPSETEGS.F.
Retrocopy IVCSFLYKNEDEEMVASASDKPLEL-EE<KIQMKDSSNLSCEQEKPLHVDIEDSGPLHDIPSETEGSVFT

Parental  ETQ
          ETQ
Retrocopy ETQ

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	0.02 RPM	5.06 RPM
SRP051959_heart	0.02 RPM	3.14 RPM
SRP051959_kidney	0.04 RPM	6.63 RPM
SRP051959_liver	0.00 RPM	2.95 RPM
SRP051959_lung	0.02 RPM	2.88 RPM
SRP051959_lymph_node	0.00 RPM	3.81 RPM
SRP051959_skeletal_muscle	0.00 RPM	3.93 RPM
SRP051959_spleen	0.00 RPM	3.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3118 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3118 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3118 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3714
Pan troglodytes	retro_ptro_2516
Gorilla gorilla	retro_ggor_2511
Macaca mulatta	retro_mmul_1700

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003535	1 retrocopy	retro_amel_370,
Callithrix jacchus	ENSCJAG00000005248	2 retrocopies	retro_cjac_3118 , retro_cjac_4098,
Dasypus novemcinctus	ENSDNOG00000014270	4 retrocopies	retro_dnov_1228, retro_dnov_1654, retro_dnov_377, retro_dnov_931,
Homo sapiens	ENSG00000155115	3 retrocopies	retro_hsap_3714, retro_hsap_4728, retro_hsap_4735,
Gorilla gorilla	ENSGGOG00000010681	1 retrocopy	retro_ggor_2511,
Myotis lucifugus	ENSMLUG00000013919	1 retrocopy	retro_mluc_897,
Macaca mulatta	ENSMMUG00000012709	3 retrocopies	retro_mmul_1700, retro_mmul_2520, retro_mmul_2524,
Monodelphis domestica	ENSMODG00000017924	1 retrocopy	retro_mdom_876,
Mustela putorius furo	ENSMPUG00000010179	1 retrocopy	retro_mputfur_182,
Nomascus leucogenys	ENSNLEG00000012846	3 retrocopies	retro_nleu_1237, retro_nleu_2122, retro_nleu_2552,
Pan troglodytes	ENSPTRG00000018502	3 retrocopies	retro_ptro_2516, retro_ptro_3145, retro_ptro_3149,