RetrogeneDB ID: retro_cjac_2990

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:75121744..75122369(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2F2
• Ensembl ID: ENSCJAG00000019220
• Aliases: None
• Description: general transcription factor IIF, polypeptide 2, 30kDa [Source:HGNC Symbol;Acc:4653]

Sequence

>retro_cjac_2990
CAACTCAACTTGGAAGCAATCCAACAGAACAGCTGTTGTGGCTAGTGGAGGTTCCCAAATACCTGTCATAAGAGTGGTCT
GAAGCTTCTGGAAGCAGTGAAGTAGGGAAGCTGCAGACTGCCAAGAATCAAAGAAAGTCTGCGCTGTCATTTACTTTGAA
TGAGGATCTTAAAAACATTCACGATATTGATGGACAACCCACCCAGTCAGCACGCCTAGGGAGGCTCCATTTCTTGTGCA
GGGGCTCAGAGGGCAGATCCTCAGTGTTGACTGAGCGTGCGCCGAGTAAGCTCTCACTGGAAGGAACAGTACAGCGAGGG
GAATGCCAACCAGCTACAAATTAAAACTCCATGAGACGGAAGAGAATGCAAACACAGGAATCTGCCAAATCTGCCAAAAC
CCTGCAGACACTGGACAAGGTTGTCACAGCCGGTTATAAACCTGTTGCTAATCATCAGTATAATACTGCATATGAGAAGA
AAAAGAAAGAAGAGGGAAAGAGGGTGCAGGCTGATAAGGACCAGGTTTTATTCTTGCTATTTGCTGCCTTTGAGAAACAC
CAGTATTACAACATAAAGGATACAGTTGGCATCACTGTGCAACCTGTGTGTGCCTCAAGGAAATC

Alignment

ORF - retro_cjac_2990 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.14 %
• Parental protein coverage: 84.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ELDLTGAKQNTG-VWLVKVPKYLSQQWAKAPGRGEVGKLRIAKNQGRTEVSFTLNEDLANIHDIGGKPAS
          .L.L....QN....WLV.VPKYLS..W..A.G..EVGKL..AKNQ.....SFTLNEDL.NIHDI.G.P..
Retrocopy QLNLEAIQQNSC<LWLVEVPKYLS*EWSEASGSSEVGKLQTAKNQRKSALSFTLNEDLKNIHDIDGQPTQ

Parental  -VSAPREHP-FVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPAASENYMRLKRLQIEESSKPVRLS
          .VS.PRE.P.F......G....V.TE....KLSLEG..VQR.EC.PA...N.MR.KR.Q...........
Retrocopy <VSTPREAP>FLCRGSEGRS-SVLTERAPSKLSLEG-TVQRGECQPATN*NSMRRKRMQTQXXXXXXXTL

Parental  QQLDKVVTTNYKPVANHQYNIEYERKKKEDGKRARADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPV-V
          Q.LDKVVT..YKPVANHQYN..YE.KKKE.GKR..ADK..VL..LF.AFEKHQYYN.KD.V.IT.QPV.V
Retrocopy QTLDKVVTAGYKPVANHQYNTAYEKKKKEEGKRVQADKDQVLFLLFAAFEKHQYYNIKDTVGITVQPV<V

Parental  YLKEI
          .LKEI
Retrocopy CLKEI

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	10.45 RPM
SRP051959_heart	0.00 RPM	7.21 RPM
SRP051959_kidney	0.00 RPM	7.92 RPM
SRP051959_liver	0.00 RPM	8.92 RPM
SRP051959_lung	0.00 RPM	9.21 RPM
SRP051959_lymph_node	0.00 RPM	13.99 RPM
SRP051959_skeletal_muscle	0.00 RPM	13.95 RPM
SRP051959_spleen	0.11 RPM	12.84 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2990 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2990 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2990 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_368
Pan troglodytes	retro_ptro_288
Gorilla gorilla	retro_ggor_379
Macaca mulatta	retro_mmul_483

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000028333	1 retrocopy	retro_acar_174,
Choloepus hoffmanni	ENSCHOG00000007391	1 retrocopy	retro_chof_1718,
Callithrix jacchus	ENSCJAG00000019220	2 retrocopies	retro_cjac_1351, retro_cjac_2990 ,
Homo sapiens	ENSG00000188342	2 retrocopies	retro_hsap_2990, retro_hsap_368,
Gorilla gorilla	ENSGGOG00000006657	2 retrocopies	retro_ggor_2070, retro_ggor_379,
Myotis lucifugus	ENSMLUG00000010505	1 retrocopy	retro_mluc_58,
Macaca mulatta	ENSMMUG00000012634	2 retrocopies	retro_mmul_1913, retro_mmul_483,
Monodelphis domestica	ENSMODG00000025484	1 retrocopy	retro_mdom_231,
Nomascus leucogenys	ENSNLEG00000002097	1 retrocopy	retro_nleu_2440,
Nomascus leucogenys	ENSNLEG00000002106	1 retrocopy	retro_nleu_742,
Otolemur garnettii	ENSOGAG00000012517	1 retrocopy	retro_ogar_2772,
Procavia capensis	ENSPCAG00000005868	3 retrocopies	retro_pcap_102, retro_pcap_173, retro_pcap_375,
Pongo abelii	ENSPPYG00000005333	1 retrocopy	retro_pabe_93,
Pan troglodytes	ENSPTRG00000005840	3 retrocopies	retro_ptro_2022, retro_ptro_288, retro_ptro_2932,
Rattus norvegicus	ENSRNOG00000029316	1 retrocopy	retro_rnor_1288,
Ictidomys tridecemlineatus	ENSSTOG00000006891	1 retrocopy	retro_itri_19,