RetrogeneDB ID: retro_cjac_1697

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:12183414..12184740(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000015738
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CRBN
• Ensembl ID: ENSCJAG00000015479
• Aliases: None
• Description: cereblon [Source:HGNC Symbol;Acc:30185]

Sequence

>retro_cjac_1697
ATGGCCGGCGAGGGAGACCAGCAGGACGCTGCGCACAACATGGGCAAACACCTGCCGCTCCTGCCTGCAGAGAGTGAGGA
AGAAGATGAAATGGAAGTTGAAGACCAGGATAGTAAAGAAGCCAAAAAACCAAACATTGTAAATTTTGACACCAGCCTGC
CAACATCACATACATACCTAGGCGCTGATATGGAAGAATTTCATGGCAGGACTTTGCACGATGACGACAGCTGTCAGGTG
ATTCCAGTTCTGCCACAGGTGATGATGATTCTGATGCCTGGACAGACATTACCTCTTCAACTTTTTCACCCTCAAGAAGT
CAGTATGGTGCGGAATTTAATTCAGAAAGATAGAACCTTTGCTGTTCTTGCATACAGCAATATACAAGAAAGGGAAGCAC
AGTTTGGAACAACAGCAGAGATATATGCCTATCGAGAAGAACAGGATTTTGGAATTGAGATAGTGAAAGTGAAAGCAATT
GGAAGACAAAGGTTCAAAGTCCTTGAGCTAAGAACACAGTCAGATGGAATCCAGCAAGCTAAAGTGCAAATTCTTCCCGA
ATGTGTGTTGCCTTCAACCATGTCTGCAGTTCAGTTAGAATCCCTCAATAAATGCCAGATATTTCCTTCAAAACCTGTCT
CATGGGAAGACCAGTGTTCATATAAATGGTGGCAGAAATACCAGAAGAGAAAGTTTCATTGTGCAAATCTAACTTCATGG
CCTCGCTGGCTGTATTCCTTATATGATGCTGAAACCTTAATGGACAGAATCAAGAAACAGCTACGTGAATGGGATGAAAA
TCTAAAAGATGATTCTCTTCCTTCAAATCCAATAGATTTTTCTTACAGAGTAGCTGCTTGTCTTCCTATTGATGATGTAT
TGAGAATTCAGCTCCTTAAAATTGGCAGTGGTATCCAGCGACTTCGCTGTGAATTAGACATTATGAATAAATGCACCTCC
CTTTGCTGTAAACAATGTCAAGAAACAGAAATAACAACGAAAAATGAAATATTCAGTTTATCCTTATGTGGGCCGATGGC
AGCTTATGTGAATCCTCATGGATATGTGCATGAGACACTTACTGTGTATAAGGCTTGCAACTTGAATCTGATAGGCCGGC
CTTCTACGGAACACAGCTGGTTTCCTGGGTATGCCTGGACTGTTGCCCAGTGTAAGATCTGTGCAAGCCATATTGGATGG
AAGTTTACAGCCACCAAAAAAGACATGTCACCTCCAAAATTTTGGGGCTTAACGCGATCTGCTCTGTTGCCTACAATCCC
AGACACGGAAGATGAAATAAGTCCAGACAAAGTAATACTTTGCTTG

Alignment

ORF - retro_cjac_1697 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGEGDQQDAAHNMGNHLPLLPAESEEEDEMEVEDQDSKEAKKPNIINFDTSLPTSHTYLGADMEEFHGR
          MAGEGDQQDAAHNMG.HLPLLPAESEEEDEMEVEDQDSKEAKKPNI.NFDTSLPTSHTYLGADMEEFHGR
Retrocopy MAGEGDQQDAAHNMGKHLPLLPAESEEEDEMEVEDQDSKEAKKPNIVNFDTSLPTSHTYLGADMEEFHGR

Parental  TLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNIQEREAQFGTTAE
          TLHDDDSCQVIPVLPQVMMIL.PGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNIQEREAQFGTTAE
Retrocopy TLHDDDSCQVIPVLPQVMMILMPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNIQEREAQFGTTAE

Parental  IYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPS
          IYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPS
Retrocopy IYAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPS

Parental  KPVSWEDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDF
          KPVSWEDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDF
Retrocopy KPVSWEDQCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDF

Parental  SYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYV
          SYRVAACLPIDDVLRIQLLKIGS.IQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYV
Retrocopy SYRVAACLPIDDVLRIQLLKIGSGIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYV

Parental  NPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLTRS
          NPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSP.KFWGLTRS
Retrocopy NPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPPKFWGLTRS

Parental  ALLPTIPDTEDEISPDKVILCL
          ALLPTIPDTEDEISPDKVILCL
Retrocopy ALLPTIPDTEDEISPDKVILCL

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	0.07 RPM	11.71 RPM
SRP051959_heart	0.04 RPM	23.40 RPM
SRP051959_kidney	0.07 RPM	23.16 RPM
SRP051959_liver	0.04 RPM	13.65 RPM
SRP051959_lung	0.21 RPM	20.66 RPM
SRP051959_lymph_node	0.16 RPM	20.71 RPM
SRP051959_skeletal_muscle	0.13 RPM	19.76 RPM
SRP051959_spleen	0.15 RPM	22.44 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1697 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1697 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1697 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015479	1 retrocopy	retro_cjac_1697 ,