RetrogeneDB ID: retro_cjac_2224

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:28916339..28917434(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000032090
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_2224
TTATCCTCTGCAGTGTGGCCAGGCGAAGAAATTGAAGCACTTACTCATTTGGAAAGAAAAGCTTGGGTGGCAAACTTTGA
AAGACCTTGAATAAATGCAAACTCTCTGCTTGGAAGCCCTACTGGACTTGGTCCCTATCTCCGATTTGGCTGTTTGTCAT
GTCGGCTGTTTTACTTCCAACTAACAGATCTCTACCAAAGGGTAAAGAAGAGCAGCTCCCCTCCCCTTTCCCTTTATGGG
AAACTGCTATGGCGTGAGTTTTTCTATACCACAGCAACAAATAATCCACGCTTCGATAAAATGGAAGGAAACCCTATCTG
TGTTCAGATTCCTTGGGATAAAAATTCTCAGGCTTTAGCCAAGTGGGCAGAAGGCAGAACAGGCTTTCCCTGGATTGATG
CCATCGTGACTCAGCTTCCTCAGGAGGGCTGGATTCATCATCTAGCCAGGCATGCAGTTGCTTGCTTCCTGACACGGGGA
ACCTGTGGATTAGTTGGGAAGAAGGAATGAAGGTATTTGAAGAATGATTGCTTGATGCAGATTGGAGCATAAATGCTGGA
AGTTGGATGTGGCTGTCTTGTAATTCCTTTATTCAACAGTTTTTTTCACTGCTATTACCTTCTTGGTTTTGGTAGAACAG
ATCCTAATGGAGACTATATCAGGTGTTATTTGCCTGTCCTAAGAGGCTTCCCTGCAAAATATATCGATGATCCCTGGAAT
GCACCAGAAGGTATCCAAAAGGTAGCCAAATGTTTGATAGGAGTTAATTATCCTAAACCAGTGGTGAAGCATGCTGAGGC
AAGTCGTTTGAATATTGAAAGAATGAAACAGATCTATCAGCAGCTTTCACAATATAGAGGACTAGGCCTTCTAGCTTCAG
TACCTTCTAATCCTAGTAGGAATGGAAGCTCCATGGGATATTCTGGAGAAAAAATCCCAGGCTGTAGCAGCAGTGGACGT
TGCTCTCAAGGGAGTGGTATTTTACACTGTGCCCATGGCGACATTCAGCAAACTCACCTATTGAAGCAAGGAAGAAGGTC
AATGAGCACTGGTCTTAGTGGTGGGAAACATCCTAGTCAGGAAGAGGACACACAG

Alignment

ORF - retro_cjac_2224 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.13 %
• Parental protein coverage: 63.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LSSAVWPGGETEALTRLERHLERKAWVANFERPRMNANSLLASPTGLSPYLRFGCLSCRLFYFKLTDLYK
          LSSAVWPG.E.EALT....HLERKAWVANFERP..NANSLL.SPTGL.PYLRFGCLSCRLFYF.LTDLY.
Retrocopy LSSAVWPGEEIEALT----HLERKAWVANFERP*INANSLLGSPTGLGPYLRFGCLSCRLFYFQLTDLYQ

Parental  KVKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPWIDAIM
          .VKK.SSPPLSLYG.LLWREFFYT.ATNNPRFDKMEGNPICVQIPWDKN..ALAKWAEGRTGFPWIDAI.
Retrocopy RVKKSSSPPLSLYGKLLWREFFYTTATNNPRFDKMEGNPICVQIPWDKNSQALAKWAEGRTGFPWIDAIV

Parental  TQLRQEGWIHHLARHAVACFLTR-GDLWISWEEGMKVFEELLLDADWSINAGSWMWLSCSSFFQQ-FFHC
          TQL.QEGWIHHLARHAVACFLTR.G.LWISWEEGMKVFEE.LLDADWSINAGSWMWLSC.SF.QQ.FFHC
Retrocopy TQLPQEGWIHHLARHAVACFLTR<GNLWISWEEGMKVFEE*LLDADWSINAGSWMWLSCNSFIQQ>FFHC

Parental  YCPVGFGRRTDPNGDYIRRRYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEASRLNI
          Y...GFG.RTDPNGDYI.R.YLPVLRGFPAKYI.DPWNAPEGIQKVAKCLIGVNYPKP.V.HAEASRLNI
Retrocopy YYLLGFG-RTDPNGDYI-RCYLPVLRGFPAKYIDDPWNAPEGIQKVAKCLIGVNYPKPVVKHAEASRLNI

Parental  ERMKQIYQQLSRYRGLGLLASVPSNPNGNGGFMGYSAENIPGCTSSGSCSQGSGILHCAHGDSQQTHLLK
          ERMKQIYQQLS.YRGLGLLASVPSNP..NG..MGYS.E.IPGC.SSG.CSQGSGILHCAHGD.QQTHLLK
Retrocopy ERMKQIYQQLSQYRGLGLLASVPSNPSRNGSSMGYSGEKIPGCSSSGRCSQGSGILHCAHGDIQQTHLLK

Parental  QGRSSMSTGISGGKRPSQEEDTQ
          QGR.SMSTG.SGGK.PSQEEDTQ
Retrocopy QGRRSMSTGLSGGKHPSQEEDTQ

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_2224 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2224 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2224 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,