RetrogeneDB ID: retro_cjac_3377

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01176866.1:7468..7953(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPS1
• Ensembl ID: ENSCJAG00000014969
• Aliases: None
• Description: RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]

Sequence

>retro_cjac_3377
GCCAGTGGTAGCAGCAGCACCAGGTCTCACTTCAGTTGGATTTCCAGCTCAGGCTCCAGCGCCAGCACTGGCTCCAGCAG
TAGCTCCAGCAATTCCTCAGCATCCAGTCACTCAGGAAGTTCTAGCATCTCCCACAGCTCCAGCAGCTCCTCAGGCTCTC
CAATTTCTTCTTGACACAGAGACAACAACAGGTGGCATCCCCGCTCCATGTCCAAACCACCTGAAAGAAATTTAAAGAAG
AGGAAAAGGTGGAGCCCATTCTCTAAGCCCACCAAAGTGCACACGAGAGACTCACCAGGAATGTGACCAAGAATCACATC
AGGGAGGTATTTTCCATCCATGGGAAAATTAAAATGATTAGCATGCCTGTGGATAGGTTACATCCCCATCTGTCCAAAGG
CTCTGCATATGTAGAGTTTGAGAATCTAGATGAAGCTCAGAATGCACTGGAGCACATGGACAGGGGACAAATAGATGGCC
AGGAG

Alignment

ORF - retro_cjac_3377 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.52 %
• Parental protein coverage: 53.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SSGSSSTRSRSSSTSSSGSSTSTGSSSGSSSSSASSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRRRSR
          .SGSSSTRS..S..SSSGSS.STGSSS.SS.SSASS.SGSSS.S.SSSSSS..GSP..S..R..NR...R
Retrocopy ASGSSSTRSHFSWISSSGSSASTGSSSSSSNSSASSHSGSSSISHSSSSSS--GSPISS*HRDNNRWHPR

Parental  SKSKPPKRDEKERKRRSPSPKPTKVHIG-RLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAY
          S.SKPP.R..K.RKR.SP..KPTKVH...RLTRNVTK.HI.E.FS..GKIKMI.MPV.R.HPHLSKG.AY
Retrocopy SMSKPPERNLKKRKRWSPFSKPTKVHTR<RLTRNVTKNHIREVFSIHGKIKMISMPVDRLHPHLSKGSAY

Parental  VEFENPDEAEKALKHMDGGQIDGQE
          VEFEN.DEA..AL.HMD.GQIDGQE
Retrocopy VEFENLDEAQNALEHMDRGQIDGQE

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	11.80 RPM
SRP051959_heart	0.00 RPM	18.45 RPM
SRP051959_kidney	0.00 RPM	15.31 RPM
SRP051959_liver	0.00 RPM	9.51 RPM
SRP051959_lung	0.00 RPM	24.19 RPM
SRP051959_lymph_node	0.00 RPM	31.51 RPM
SRP051959_skeletal_muscle	0.00 RPM	23.21 RPM
SRP051959_spleen	0.00 RPM	19.20 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3377 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3377 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3377 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014969	2 retrocopies	retro_cjac_2127, retro_cjac_3377 ,
Equus caballus	ENSECAG00000023288	1 retrocopy	retro_ecab_524,
Gorilla gorilla	ENSGGOG00000014275	1 retrocopy	retro_ggor_2016,
Macropus eugenii	ENSMEUG00000008882	1 retrocopy	retro_meug_1996,
Myotis lucifugus	ENSMLUG00000016808	3 retrocopies	retro_mluc_2237, retro_mluc_2618, retro_mluc_643,
Monodelphis domestica	ENSMODG00000015891	1 retrocopy	retro_mdom_1171,
Mus musculus	ENSMUSG00000034681	1 retrocopy	retro_mmus_173,
Oryctolagus cuniculus	ENSOCUG00000004387	2 retrocopies	retro_ocun_1544, retro_ocun_1745,
Otolemur garnettii	ENSOGAG00000031582	1 retrocopy	retro_ogar_3241,
Rattus norvegicus	ENSRNOG00000008703	4 retrocopies	retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii	ENSSHAG00000016951	1 retrocopy	retro_shar_390,
Ictidomys tridecemlineatus	ENSSTOG00000013200	1 retrocopy	retro_itri_1160,