RetrogeneDB ID: retro_cjac_2223

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:28844926..28845921(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CRY1
• Ensembl ID: ENSCJAG00000015099
• Aliases: None
• Description: None

Sequence

>retro_cjac_2223
AATCTGCTTGGAAGCCCTACTGGACTTGGTCCTTAACTCCGATTTGGCTGTTTGTCATGTCGGCTGTTTTACTTCCAACT
AACAGACCTCTACCAAAAGGTAAAGAAGAGCAGTTCTCTTCCCCTTTCCCTTTATGGGCAACTGCTATGGTGTGAGTTTT
TCTATATAGCAGCAACAAATAATCCACGCTTCGATAAAATGGAAGGAAACCCTATCTGTGTTCAGATTCCTTGGGATAAA
AATTCTCAGGCTTTAGCCAAATGAGCAGAAGGCAGGACAGGCTTTCCCTGGATTGATGCCATCGTGACTCAGCTTCCTCA
GGAGGGCTGGATTCATCATCTAGCCAGGCATGCAGTTGCTTGCTTCCTGACACGGGGGACCTGTGGATTCGTTGGGAAGA
AAGAATGAAGGTATTTGAAGAATGATTGCTTGATGCAGATTGGAGCATAAATGCTGGAAGTTGGATGTGGCTGTCTTGTA
ATTCCTTTTTTCAACAGTTTTTTCACTGCTATTACCCTGTTGGTTTTGGTAGGAGAACAAATCCTAATGGAGACTATATC
AGGTGTTATTTGCCTGTCCTAAGAGGCTTCCCTGCAAAATATATCGATGATCCCTGGAATGCACCAGAAGGTATCCAAAA
GGTAGCCAAATGTTTGATAGGAGTTAATTATCCTAAACCAGTGGTGAAGCATGCTGAGGCAAGTCGTTTGAATATTGAAA
GAATGAAACAGATCTATCAGCAGCTTTCACAATATAGAGGACTAGGTCTTCTAGCTTCAGTACCTTCTAATCCTAGTAGG
AATGGAAGCTTCATGGGATATTCTACAGAAAATATCCCAGGCTGTCGCAGCAGTGGACGTTGCTCTCAGGGGAGTGGTAT
TTTACACTGTGCCCATGGCGACATTCAGCAAACTCACCTATTGAAGCAAGGAAGAAGGTCCATGAGCACTGGTCTTAGTG
GTGGGAAACATCCTAGTCAGGAAGAGGACACACAG

Alignment

ORF - retro_cjac_2223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.62 %
• Parental protein coverage: 56.73 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLLASPTGLSPYLRFGCLSCRLFYFKLTDLYKKVKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGN
          .LL.SPTGL.P.LRFGCLSCRLFYF.LTDLY.KVKK.SS.PLSLYGQLLW.EFFY.AATNNPRFDKMEGN
Retrocopy NLLGSPTGLGP*LRFGCLSCRLFYFQLTDLYQKVKKSSSLPLSLYGQLLWCEFFYIAATNNPRFDKMEGN

Parental  PICVQIPWDKNPEALAKWAEGRTGFPWIDAIMTQLRQEGWIHHLARHAVACFLTRG-DLWISWEEGMKVF
          PICVQIPWDKN..ALAK.AEGRTGFPWIDAI.TQL.QEGWIHHLARHAVACFLTRG.DLWI.WEE.MKVF
Retrocopy PICVQIPWDKNSQALAK*AEGRTGFPWIDAIVTQLPQEGWIHHLARHAVACFLTRG<DLWIRWEERMKVF

Parental  EELLLDADWSINAGSWMWLSCSSFFQQFFHCYCPVGFGRRTDPNGDYIRRRYLPVLRGFPAKYIYDPWNA
          EE.LLDADWSINAGSWMWLSC.SFFQQFFHCY.PVGFGRRT.PNGDYIR..YLPVLRGFPAKYI.DPWNA
Retrocopy EE*LLDADWSINAGSWMWLSCNSFFQQFFHCYYPVGFGRRTNPNGDYIRC-YLPVLRGFPAKYIDDPWNA

Parental  PEGIQKVAKCLIGVNYPKPMVNHAEASRLNIERMKQIYQQLSRYRGLGLLASVPSNPNGNGGFMGYSAEN
          PEGIQKVAKCLIGVNYPKP.V.HAEASRLNIERMKQIYQQLS.YRGLGLLASVPSNP..NG.FMGYS.EN
Retrocopy PEGIQKVAKCLIGVNYPKPVVKHAEASRLNIERMKQIYQQLSQYRGLGLLASVPSNPSRNGSFMGYSTEN

Parental  IPGCTSSGSCSQGSGILHCAHGDSQQTHLLKQGRSSMSTGISGGKRPSQEEDTQ
          IPGC.SSG.CSQGSGILHCAHGD.QQTHLLKQGR.SMSTG.SGGK.PSQEEDTQ
Retrocopy IPGCRSSGRCSQGSGILHCAHGDIQQTHLLKQGRRSMSTGLSGGKHPSQEEDTQ

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	12.31 RPM
SRP051959_heart	0.00 RPM	9.56 RPM
SRP051959_kidney	0.00 RPM	8.08 RPM
SRP051959_liver	0.00 RPM	6.52 RPM
SRP051959_lung	0.00 RPM	13.62 RPM
SRP051959_lymph_node	0.00 RPM	11.94 RPM
SRP051959_skeletal_muscle	0.00 RPM	12.71 RPM
SRP051959_spleen	0.00 RPM	9.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2223 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2223 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2223 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015099	3 retrocopies	retro_cjac_2223 , retro_cjac_2224, retro_cjac_3842,