RetrogeneDB ID: retro_cjac_1980

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:185820246..185820868(-)
• Located in intron of: ENSCJAG00000033957

Retrocopy information

• Ensembl ID: ENSCJAG00000011820
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TAF11
• Ensembl ID: ENSCJAG00000015388
• Aliases: None
• Description: TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa [Source:HGNC Symbol;Acc:11544]

Sequence

>retro_cjac_1980
ATGGACTGGATCCGCATCTCAGCCATGGAGACAGGCAGGCAAACAGGTGTGTCTGCTGAGATGTTCACCATGCCTTGAGG
TCTGGAGGCCAGCAACAAGGATGGAATCCCAGAGGATCTAGATGGGAACTTGGAAGAACCCATGGATCAGGAAGGTAAGC
TCAGGAGTCGGGACGTTATGGACCTCACAGCAGATGACAAGGAAGCCTCAGCCTCAGGTCCTCCTGCATCCAAAAGACTG
AAAACAGATACCAAAGGAAAGAAGGAGAGGAAGCCCACGGTGGATGAAGATGAGGCTCAGAGGATGACAAACCTCCTGTC
TGCTATGTCTGAGGAGCAGCTGGCCCGCTATGAGGTGTGTCGCCGGTCAGCTTTCCCAAAAACACGCATTGCAAATCTGA
TGCAGTCTATCACTGGCAGGTCAGTGCCTGAGAATGTGACCATTGCTATGGCTGGAATAGCCAAGGTCTTGGTGGGAGAG
GTGGTGGAAGAGGCCCTGGACGTGTGTGAGATGTGGGGAGAAACGCCCCCGCTGCAGCCCAGGCATTTGAGGGAGGCTGT
TCGCAGGTTAAAGTCCAAGGGCCTCTTCCCCCAACACCAAGTACAAGAAAATCATGTTCTTC

Alignment

ORF - retro_cjac_1980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDDARESPTDKGGETGESDETVAAPGDPGATDTDGIPEETDGDADADLKEAAAEEGELKSQDVSDLTAVE
          MD..R.S....G..TG.S.E....P....A...DGIPE..DG.....L.E....EG.L.S.DV.DLTA..
Retrocopy MDWIRISAMETGRQTGVSAEMFTMP*GLEASNKDGIPEDLDGN----LEEPMDQEGKLRSRDVMDLTADD

Parental  REDSSLLTPAAKKLKIDTKEKKEKKQKVDEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQS
          .E.S....PA.K.LK.DTK.KKE.K..VDEDE.Q.M..L.S..SEEQL.RYE..RRSAFPK..I..L.QS
Retrocopy KEASASGPPASKRLKTDTKGKKERKPTVDEDEAQRMTNLLSAMSEEQLARYEVCRRSAFPKTRIANLMQS

Parental  ITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKG-QIPNSKHKKII
          ITG.SV..NV.IAM.GI.KV.VGEVVEEALDVCE.WGE.PPLQP.H.REAVRRLKSKG...PN.K.KKI.
Retrocopy ITGRSVPENVTIAMAGIAKVLVGEVVEEALDVCEMWGETPPLQPRHLREAVRRLKSKG>SSPNTKYKKIM

Parental  FF
          FF
Retrocopy FF

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	5.37 RPM
SRP051959_heart	0.00 RPM	5.67 RPM
SRP051959_kidney	0.00 RPM	4.84 RPM
SRP051959_liver	0.00 RPM	5.00 RPM
SRP051959_lung	0.00 RPM	5.16 RPM
SRP051959_lymph_node	0.00 RPM	5.09 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.47 RPM
SRP051959_spleen	0.00 RPM	5.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1980 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1980 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1980 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016887	1 retrocopy	retro_btau_218,
Callithrix jacchus	ENSCJAG00000015388	5 retrocopies	retro_cjac_1342, retro_cjac_1980 , retro_cjac_2310, retro_cjac_2402, retro_cjac_2657,
Cavia porcellus	ENSCPOG00000015428	1 retrocopy	retro_cpor_629,
Dipodomys ordii	ENSDORG00000009352	1 retrocopy	retro_dord_4,
Equus caballus	ENSECAG00000016725	1 retrocopy	retro_ecab_83,
Felis catus	ENSFCAG00000022931	1 retrocopy	retro_fcat_1628,
Homo sapiens	ENSG00000064995	15 retrocopies	retro_hsap_3139, retro_hsap_3140, retro_hsap_3141, retro_hsap_3142, retro_hsap_3143, retro_hsap_3144, retro_hsap_3145, retro_hsap_3146, retro_hsap_3147, retro_hsap_3148, retro_hsap_3149, retro_hsap_3295, retro_hsap_3296, retro_hsap_3297, retro_hsap_3298,
Loxodonta africana	ENSLAFG00000011482	1 retrocopy	retro_lafr_1108,
Microcebus murinus	ENSMICG00000014063	1 retrocopy	retro_mmur_1196,
Myotis lucifugus	ENSMLUG00000001766	1 retrocopy	retro_mluc_87,
Nomascus leucogenys	ENSNLEG00000008457	29 retrocopies	retro_nleu_149, retro_nleu_151, retro_nleu_152, retro_nleu_1742, retro_nleu_1743, retro_nleu_2976, retro_nleu_2977, retro_nleu_2998, retro_nleu_3041, retro_nleu_3042, retro_nleu_3043, retro_nleu_3044, retro_nleu_3049, retro_nleu_3050, retro_nleu_3051, retro_nleu_3053, retro_nleu_3054, retro_nleu_3055, retro_nleu_3081, retro_nleu_3082, retro_nleu_3083, retro_nleu_3084, retro_nleu_3093, retro_nleu_3094, retro_nleu_3109, retro_nleu_3113, retro_nleu_3120, retro_nleu_3125, retro_nleu_3127,
Otolemur garnettii	ENSOGAG00000008522	2 retrocopies	retro_ogar_3055, retro_ogar_922,
Pongo abelii	ENSPPYG00000016521	1 retrocopy	retro_pabe_200,
Pan troglodytes	ENSPTRG00000018075	9 retrocopies	retro_ptro_2123, retro_ptro_2124, retro_ptro_2125, retro_ptro_2126, retro_ptro_2127, retro_ptro_2128, retro_ptro_2129, retro_ptro_2130, retro_ptro_2977,
Tursiops truncatus	ENSTTRG00000007855	1 retrocopy	retro_ttru_1063,