RetrogeneDB ID: retro_cjac_3928

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286273.1:14668..15229(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRNAU1AP
• Ensembl ID: ENSCJAG00000009717
• Aliases: None
• Description: tRNA selenocysteine 1 associated protein 1 [Source:HGNC Symbol;Acc:30813]

Sequence

>retro_cjac_3928
TTTGTGGGGGACCTAACCCCAGATGTGGAAGATGGCATGCTGTATGAATTCTTCATCAAAGTCTATCCCTCCTGTCGGGG
AGGCAAGCTGGTTTTGGACCAGACAGGTGTGTCTAAGGGTTATGGTTTTGTGAAATTCACAGTTGAACTGGAACAGACAC
GAGCCCTGATGGAGTGCCAGGGAGCAGTGGGACTGGGGTCTAAACCTGTGCAGCTGGGCGCAGCAATCCCTAAAGCGAGC
TGTGTAAAGCCAGTGGAATATAGTCAGATGTACAGTTACAGCTAAAATCAGTATTACCAGCAGTACCAGAACTACTATGC
TCAGTGGGGCTATGACCAAAACACAGGCAGCTACAGCTACAGTTACCCCCAGTATGGCTATACTCAGAGCACCATGCAGA
CATATGAAGAAGTTGGAGACAATGCATTGGAAGACCCCATGCCACAGCTGGATGTGACTGAGGCCAACAAGGAGTTCATG
GAACAGAGTGAGGAGCTGTATGACGCTCTGATGAATTGGCAGCCCCTGGACACAGTGTCTTCAGAGATCCCTGCCATGAT
G

Alignment

ORF - retro_cjac_3928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.06 %
• Parental protein coverage: 65.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPV
          FVGDLTPDV.DGMLYEFF.KVYPSCRGGK.VLDQTGVSKGYGFVKFT.ELEQ.RAL.ECQGAVGLGSKPV
Retrocopy FVGDLTPDVEDGMLYEFFIKVYPSCRGGKLVLDQTGVSKGYGFVKFTVELEQTRALMECQGAVGLGSKPV

Parental  RLSVAIPKASRVKPVEYSQMYSYSYNQYYQQYQNYYAQWGYDQNTGSYSYSYPQYGYTQSTMQTYEEVGD
          .L..AIPKAS.VKPVEYSQMYSYS.NQYYQQYQNYYAQWGYDQNTGSYSYSYPQYGYTQSTMQTYEEVGD
Retrocopy QLGAAIPKASCVKPVEYSQMYSYS*NQYYQQYQNYYAQWGYDQNTGSYSYSYPQYGYTQSTMQTYEEVGD

Parental  DALEDPMPQLDVTEANKEFMEQSEELYDALMDCHWQPLDTVSSEIPAMM
          .ALEDPMPQLDVTEANKEFMEQSEELYDALM...WQPLDTVSSEIPAMM
Retrocopy NALEDPMPQLDVTEANKEFMEQSEELYDALM--NWQPLDTVSSEIPAMM

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	5.70 RPM
SRP051959_heart	0.02 RPM	4.40 RPM
SRP051959_kidney	0.00 RPM	4.13 RPM
SRP051959_liver	0.00 RPM	3.90 RPM
SRP051959_lung	0.00 RPM	5.11 RPM
SRP051959_lymph_node	0.00 RPM	5.91 RPM
SRP051959_skeletal_muscle	0.00 RPM	5.68 RPM
SRP051959_spleen	0.00 RPM	4.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3928 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3928 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3928 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011367	1 retrocopy	retro_amel_1782,
Callithrix jacchus	ENSCJAG00000009717	1 retrocopy	retro_cjac_3928 ,
Equus caballus	ENSECAG00000012980	1 retrocopy	retro_ecab_452,
Mustela putorius furo	ENSMPUG00000015511	2 retrocopies	retro_mputfur_1185, retro_mputfur_856,
Pelodiscus sinensis	ENSPSIG00000006864	1 retrocopy	retro_psin_41,
Tupaia belangeri	ENSTBEG00000008049	1 retrocopy	retro_tbel_923,