RetrogeneDB ID: retro_cjac_3842

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284992.1:681..1594(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000018965
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_cjac_3842
ACAGATCTCTACCAAAGGGTAAAGAAGAGCAGTTCCCTTCCCCTTTCCCTTTATGGGAAACTGCTATGGCGTGAGTTTTT
CTACACAGCAGCAACAAATAATCCACGCTTCGATAAAATGGAAGGAAACCCTATCTGTGTTCAGATTCCTTGGGATAAAA
ATTCTCAGGCTTTAGCCAAATGGGCAGAAGGCGGGACAGGCTTTCCCTGGATTGATGCCATTGTGACTCAGCTTCCTCAG
GAGGGCTGGATATATCATCTAGCCAGGCATGCAGTTGCTTGCTTCCTGACATGGGGAACCTGTGGATTAGTTGGGAAGAA
GGAATGAAGGTATTTGAAGAATGATTGCTTGATGCAGATTGGAGCATAAATGCTGGAAGTTGGATGTGGCTATCTTGTAA
TTCCTTTTTCAACAGTTTTTTCACTGCTATTGCCCTGTTGGTTTTGGTAGGAGAACAGATCCTAATGGAGACTATATCAG
GTGTTATTTGCCTGTCCTAAGAGGCTTCCCTGCAAAATATATCGATGATCCCTGGAATGCACCAGAAGGTATTCACAAGG
TAGCCAAATGTTTGATAGGAGTTAATTATTCTAAACCAGTGGTGAAGCATGCTGAGGCAAGTCGTTTGAATATTGAAAGA
ATGAAACAGATCTATCAGCAGCTTTCACAATATAGAGGACTAGGTCTTCTAGCTTCAGTACCTTCTAATCCTAGTAGGAA
TGAAAGCTCCATGGGATATTCTACAGAAAATATCCCAGGCTGTCGCAGCAGTGGACGTTGCTCTCAAGGGAGTGGTATTT
TACACTGTGCCCATGGCGACATTCAGCAAACTCACCTATTGAAGCAAGGAAGAAGGTCCATGAGCACTGGTCTTAGTGGT
GGGAAACATCCTAGTCAGGAAGAGGACACACAG

Alignment

ORF - retro_cjac_3842 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.99 %
• Parental protein coverage: 52.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TDLYKKVKKNSSPPLSLYGQLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNPEALAKWAEGRTGFPW
          TDLY..VKK.SS.PLSLYG.LLWREFFYTAATNNPRFDKMEGNPICVQIPWDKN..ALAKWAEG.TGFPW
Retrocopy TDLYQRVKKSSSLPLSLYGKLLWREFFYTAATNNPRFDKMEGNPICVQIPWDKNSQALAKWAEGGTGFPW

Parental  IDAIMTQLRQEGWIHHLARHAVACFLT-RGDLWISWEEGMKVFEELLLDADWSINAGSWMWLSCSSFF-Q
          IDAI.TQL.QEGWI.HLARHAVACFLT..G.LWISWEEGMKVFEE.LLDADWSINAGSWMWLSC.SFF.Q
Retrocopy IDAIVTQLPQEGWIYHLARHAVACFLT<MGNLWISWEEGMKVFEE*LLDADWSINAGSWMWLSCNSFF<Q

Parental  QFFHCYCPVGFGRRTDPNGDYIRRRYLPVLRGFPAKYIYDPWNAPEGIQKVAKCLIGVNYPKPMVNHAEA
          QFFHCYCPVGFGRRTDPNGDYIR..YLPVLRGFPAKYI.DPWNAPEGI.KVAKCLIGVNY.KP.V.HAEA
Retrocopy QFFHCYCPVGFGRRTDPNGDYIRC-YLPVLRGFPAKYIDDPWNAPEGIHKVAKCLIGVNYSKPVVKHAEA

Parental  SRLNIERMKQIYQQLSRYRGLGLLASVPSNPNGNGGFMGYSAENIPGCTSSGSCSQGSGILHCAHGDSQQ
          SRLNIERMKQIYQQLS.YRGLGLLASVPSNP..N...MGYS.ENIPGC.SSG.CSQGSGILHCAHGD.QQ
Retrocopy SRLNIERMKQIYQQLSQYRGLGLLASVPSNPSRNESSMGYSTENIPGCRSSGRCSQGSGILHCAHGDIQQ

Parental  THLLKQGRSSMSTGISGGKRPSQEEDTQ
          THLLKQGR.SMSTG.SGGK.PSQEEDTQ
Retrocopy THLLKQGRRSMSTGLSGGKHPSQEEDTQ

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_3842 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3842 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3842 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 ,