RetrogeneDB ID: retro_cjac_2705

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:26557898..26558370(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000007547
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBPMS
• Ensembl ID: ENSCJAG00000012366
• Aliases: None
• Description: RNA binding protein with multiple splicing [Source:HGNC Symbol;Acc:19097]

Sequence

>retro_cjac_2705
GAGGAGGAGGTCCGGACACTGTTTGTCAGCGGCCTCCCTGTGGACATTAAACTCAGAGAACTGTACTTGCTTTTCCGGCA
GTTCAAGGGGTATGAAGGGTCCCTGATCAAGCTCACCGCGCGACAGCCTGTTGGTTTTGTGATTTTTGACAGCCGGGCAG
GAGCAGAAGCAGCCAAGAACGCGTTGAACGGTATTCGCTTCCATCCTGAGAACCCGCAGACGCTGAGGCTAGAGTTTGCC
AAAGCCAACACCAAGATGGCCAAGAGCAAGCTGATGGTGACTCCAAATCCCAGCAAGCAACATGCACCCTGCCCTAGGAG
CACAACTGATTGCACGGGACCCTTATGACCTGATGGGGGCTGCTCTGATCCCTGCATCCCCAGAGGCCTGGGCCCCCTAC
CCTTCATACACCACAGAGTTGACCCCAGCCATCTCCCGTGCTGCGTTCACCTACCCAGCTGCCACTGCCGCC

Alignment

ORF - retro_cjac_2705 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.78 %
• Parental protein coverage: 79.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEEVRTLFVSGLPLDIKPRELYLLFRPFKGYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDPE
          EEEVRTLFVSGLP.DIK.RELYLLFR.FKGYEGSLIKLT..QPVGFV.FDSR..AEAAKNALNGIRF.PE
Retrocopy EEEVRTLFVSGLPVDIKLRELYLLFRQFKGYEGSLIKLTARQPVGFVIFDSRAGAEAAKNALNGIRFHPE

Parental  IPQTLRLEFAKANTKMAKNKLVGTPN-PSTPL-PNTVPQFIAREPYELTVPALYPSSPEVWAPYPLYPAE
          .PQTLRLEFAKANTKMAK.KL..TPN.P.....P....Q.IAR.PY.L...AL.P.SPE.WAPYP.Y..E
Retrocopy NPQTLRLEFAKANTKMAKSKLMVTPN>PASNMHPALGAQLIARDPYDLMGAALIPASPEAWAPYPSYTTE

Parental  LAPALPPPAFTYPASLHA
          L.PA....AFTYPA...A
Retrocopy LTPAISRAAFTYPAATAA

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	9.23 RPM
SRP051959_heart	0.04 RPM	25.61 RPM
SRP051959_kidney	0.00 RPM	21.72 RPM
SRP051959_liver	0.00 RPM	5.44 RPM
SRP051959_lung	0.03 RPM	12.40 RPM
SRP051959_lymph_node	0.00 RPM	2.81 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.69 RPM
SRP051959_spleen	0.00 RPM	7.58 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2705 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2705 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2705 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
Ailuropoda melanoleuca	ENSAMEG00000001522	1 retrocopy	retro_amel_905,
Bos taurus	ENSBTAG00000033727	1 retrocopy	retro_btau_1555,
Callithrix jacchus	ENSCJAG00000005200	2 retrocopies	retro_cjac_1775, retro_cjac_298,
Callithrix jacchus	ENSCJAG00000012366	1 retrocopy	retro_cjac_2705 ,
Tarsius syrichta	ENSTSYG00000013982	2 retrocopies	retro_tsyr_1171, retro_tsyr_1397,