RetrogeneDB ID: retro_cjac_4112

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:103505342..103506087(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YAP1
• Ensembl ID: ENSCJAG00000000627
• Aliases: None
• Description: Yes-associated protein 1 [Source:HGNC Symbol;Acc:16262]

Sequence

>retro_cjac_4112
ATGGATCCTGGGCAGCAGCCATCATCTCAACCAGCCCACCAGGGCCAAGGGAAGCAGCCTGGACAGCCCTCCCAGGGACA
GGATCTGCCATCTGGGCCGGGGCAACCAGCAACCCCCGGCGACCCAGGCGGCACCATAGTCACTCCTCACAGTGCGCCAG
ATCATGCACATCCAAGAGGACTCGGAGACCGATCCAGAGGCACTCTTGAGCACCGTCATAAATGCTATGATGGTCAACAT
ATCCCAGACTGTGCCCATGAGGCTCTGGAAGCTGCCTGACTCCTTCAAGCAGCAGGAGCCCAAATCCCACCGCCCGACGG
GCCAGTACTGACAAAGGCTCTGCAGGAACCCTGACTCCACAGCATGTTCCAGCTTATTCCTTGCAGTTGAGAGCGGTTTC
TCCTGGGACACTGGCTCCCACTGCAGTAGTCTCTGGCCCAGGAGCTACACCCACAGCTCAACATCATTGACAGTCTTCTT
TGGAGATACTTGATGATGTATCTCTGTCAGCAGGCTGGGAGATGGTGAAGACATCTTCTGGTAAGAGATGCTTCTTAAAT
AACAGAGATCAGACAACATGGCAGGACCCCAGGAAGGCCGTGCTCTCTCAGATAAATATTACAGCCCCCACCGGTCCACC
AGTGCAGCAGAGTATGAACTTGGCCTCAGGTCCTCTTCCTGCTGGATAGGAACAAGCCATGACTCAAGTTGAAGAAATTA
TTATCTAAACCATGAAAACAAGACA

Alignment

ORF - retro_cjac_4112 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.83 %
• Parental protein coverage: 52.16 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MDPGQQPPPQAAPQGQGQPPAQP-QGQGPSSAPGQPA-PAATQAASQAPPAGHQIVHVRGDSETDLEALF
          MDPGQQP..Q.A.QGQG..P.QP.QGQ...S.PGQPA.P.ATQAA........QI.H...DSETD.EAL.
Retrocopy MDPGQQPSSQPAHQGQGKQPGQPSQGQDLPSGPGQPA>PPATQAAP*SLLTVRQIMHIQEDSETDPEALL

Parental  NAVMNPKTANVPQTVPMRLRKLPDSFFKPPEPKSH-SRQASTDAGTAGALTPQHVRAHSSPASLQLGAVS
          ..V.N....N..QTVPMRL.KLPDSF.K..EPKSH..R.ASTD.G.AG.LTPQHV.A.....SLQL.AVS
Retrocopy STVINAMMVNISQTVPMRLWKLPDSF-KQQEPKSH>ARRASTDKGSAGTLTPQHVPAY----SLQLRAVS

Parental  PGTLTPTGVVSGPAATPTAQHLRQSSFEIPDDVPLPAGWEMAKTSSGQRYFLNHIDQTTTWQDPRKAMLS
          PGTL.PT.VVSGP.ATPTAQH..QSS.EI.DDV.L.AGWEM.KTSSG.R.FLN..DQ.TTWQDPRKA.LS
Retrocopy PGTLAPTAVVSGPGATPTAQHH*QSSLEILDDVSLSAGWEMVKTSSGKRCFLNNRDQ-TTWQDPRKAVLS

Parental  QMNVTAPTSPPVQQNMMNSASGPLPDGWEQAMTQDGEI-YYINHKNKT
          Q.N.TAPT.PPVQQ..MN.ASGPLP.G.EQAMTQ..EI.YY.NH.NKT
Retrocopy QINITAPTGPPVQQS-MNLASGPLPAG*EQAMTQVEEI<YYLNHENKT

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	0.04 RPM	23.78 RPM
SRP051959_heart	0.02 RPM	37.76 RPM
SRP051959_kidney	0.07 RPM	28.22 RPM
SRP051959_liver	0.02 RPM	12.11 RPM
SRP051959_lung	0.02 RPM	34.08 RPM
SRP051959_lymph_node	0.00 RPM	6.28 RPM
SRP051959_skeletal_muscle	0.00 RPM	16.01 RPM
SRP051959_spleen	0.00 RPM	22.96 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4112 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4112 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4112 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001095	2 retrocopies	retro_chof_1687, retro_chof_407,
Callithrix jacchus	ENSCJAG00000000627	1 retrocopy	retro_cjac_4112 ,
Homo sapiens	ENSG00000137693	1 retrocopy	retro_hsap_3531,
Otolemur garnettii	ENSOGAG00000002885	2 retrocopies	retro_ogar_1565, retro_ogar_3345,
Pan troglodytes	ENSPTRG00000004211	1 retrocopy	retro_ptro_2399,