RetrogeneDB ID: retro_cjac_3862

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL285286.1:52048..52504(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023348
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UBE2A
• Ensembl ID: ENSCJAG00000005098
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2A [Source:HGNC Symbol;Acc:12472]

Sequence

>retro_cjac_3862
ATGTCCACCCTGGCTCACCGGTGCCTCATGCGGGACTTCAAGAGGTTGCAGGAGGATCCTCCAGCCACAGTCAGTGGGGC
TCCGTCCGAGAACAACATAATGGTGTGGAACGCGGTCATTTTCGGGCCTGAAGGGACCCCATTTGAGGATGGAACATTTA
AACTTACAATAGAATTCACTGAAGAATATCCAAATAAGCCACCTACAGTTAGATTTGTCTCTAAGATGTTCCATCCAAAT
GTCTATGCAGATGGTAGTATATGTCTGGATATACTTCAGAACCGTTGGAGTCCAACCTATGATGTGTCTTCGATTTTAAC
ATCCATGCAGTCTCTATTGGATGAACCCAATCCCAATAGTCCAGCAAACAGCCAGGCTGCTCAGCTGTACCAGGAGAACA
AGCGGGAATATGAAAAGCATGTTACTGCAATAGTAGAACAAAGCTAGCGCGATTGT

Alignment

ORF - retro_cjac_3862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSTPARRRLMRDFKRLQEDPPAGVSGAPSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFTEEYPNKPPTV
          MST.A.R.LMRDFKRLQEDPPA.VSGAPSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFTEEYPNKPPTV
Retrocopy MSTLAHRCLMRDFKRLQEDPPATVSGAPSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFTEEYPNKPPTV

Parental  RFVSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSIQSLLDEPNPNSPANSQAAQLYQENKREYEKR
          RFVSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTS.QSLLDEPNPNSPANSQAAQLYQENKREYEK.
Retrocopy RFVSKMFHPNVYADGSICLDILQNRWSPTYDVSSILTSMQSLLDEPNPNSPANSQAAQLYQENKREYEKH

Parental  VSAIVEQSWRDC
          V.AIVEQS.RDC
Retrocopy VTAIVEQS*RDC

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	0.11 RPM	9.65 RPM
SRP051959_heart	0.09 RPM	9.00 RPM
SRP051959_kidney	0.27 RPM	12.00 RPM
SRP051959_liver	0.06 RPM	6.54 RPM
SRP051959_lung	0.10 RPM	11.06 RPM
SRP051959_lymph_node	0.05 RPM	10.16 RPM
SRP051959_skeletal_muscle	0.07 RPM	13.50 RPM
SRP051959_spleen	0.04 RPM	10.00 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3862 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3862 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001079	1 retrocopy	retro_chof_1316,
Callithrix jacchus	ENSCJAG00000000874	3 retrocopies	retro_cjac_1995, retro_cjac_3689, retro_cjac_406,
Callithrix jacchus	ENSCJAG00000005098	2 retrocopies	retro_cjac_1180, retro_cjac_3862 ,
Cavia porcellus	ENSCPOG00000011908	1 retrocopy	retro_cpor_489,
Dasypus novemcinctus	ENSDNOG00000007060	1 retrocopy	retro_dnov_215,
Macropus eugenii	ENSMEUG00000003026	1 retrocopy	retro_meug_2180,
Monodelphis domestica	ENSMODG00000010209	1 retrocopy	retro_mdom_341,
Oryctolagus cuniculus	ENSOCUG00000016739	1 retrocopy	retro_ocun_183,
Otolemur garnettii	ENSOGAG00000024335	1 retrocopy	retro_ogar_3203,
Procavia capensis	ENSPCAG00000005045	1 retrocopy	retro_pcap_222,
Sus scrofa	ENSSSCG00000012621	1 retrocopy	retro_sscr_29,
Tarsius syrichta	ENSTSYG00000000888	1 retrocopy	retro_tsyr_676,