RetrogeneDB ID: retro_cjac_1624

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 18:4349751..4350231(+)
• Located in intron of: ENSCJAG00000006424

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPSM3
• Ensembl ID: ENSCJAG00000001882
• Aliases: None
• Description: G-protein signaling modulator 3 [Source:HGNC Symbol;Acc:13945]

Sequence

>retro_cjac_1624
ATGGAGGCTGAGAGACCACAGGAAGAAGAGGATGGTGAGCAGGACCCCCCTCAGGATGAGCAAGGCTGGCCCCCTCCAGA
TTCCACCACTCGGCCGTGGCGATCTGCTCCTCCATCCCCTCCTCCTCCACAGACCCATAACACAGCCCTGGGACCCCGCT
CGGCCTCCCTGCTCTCCCTGCAGACTGAGCTCCTTCTGGACCTGGTAGCTGAAGCCCAGTCCCGCCGCCTAGAGGAGCAG
AGGGCCACCTTTCACACCCCCCAAAACCCCCCAGTCCTAGCCCCTGCCCCACCCCGTCCTCTTGAGGACAGAGAACAGCT
CTACAGCACCATCCTCAGTCACCAGTGCCAGCGGATGGAAGCCCAGCGGTCAGAGCCTCCCCTCCCTCCAGGGGGGCAGG
AGCTCCTGGAGTTGCTGCTGAGAGTTCAGTGTGGGGGTCGAATGGAGGAGCAAAGGTCCCAGCCCCCGACACACACCTGC

Alignment

ORF - retro_cjac_1624 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEAERPQEEEDGEQDPPQDEQGWPPPNSTTRPWRSAPPSPPPPRTHNTALGPRSASLLSLQTELLLDLVA
          MEAERPQEEEDGEQDPPQDEQGWPPP.STTRPWRSAPPSPPPP.THNTALGPRSASLLSLQTELLLDLVA
Retrocopy MEAERPQEEEDGEQDPPQDEQGWPPPDSTTRPWRSAPPSPPPPQTHNTALGPRSASLLSLQTELLLDLVA

Parental  EAQSRRLEEQRATFHTPQNPPVLAPAPPRPLEDREQLYSTILSHQCQRMEAQRSEPPLPPGGQELLELLL
          EAQSRRLEEQRATFHTPQNPPVLAPAPPRPLEDREQLYSTILSHQCQRMEAQRSEPPLPPGGQELLELLL
Retrocopy EAQSRRLEEQRATFHTPQNPPVLAPAPPRPLEDREQLYSTILSHQCQRMEAQRSEPPLPPGGQELLELLL

Parental  RVQGGGRMEEQRSQPPTHTC
          RVQ.GGRMEEQRSQPPTHTC
Retrocopy RVQCGGRMEEQRSQPPTHTC

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	0.27 RPM	1.04 RPM
SRP051959_heart	0.26 RPM	0.72 RPM
SRP051959_kidney	0.27 RPM	1.26 RPM
SRP051959_liver	0.15 RPM	1.17 RPM
SRP051959_lung	0.60 RPM	5.86 RPM
SRP051959_lymph_node	0.53 RPM	10.59 RPM
SRP051959_skeletal_muscle	0.17 RPM	0.59 RPM
SRP051959_spleen	0.21 RPM	6.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1624 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1624 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1624 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001882	1 retrocopy	retro_cjac_1624 ,